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Report for CCDS42751.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
42751.2 Public Homo sapiens 2 SMPD4 24 110 108 CCDS HistoryNCBI Gene:55627Re-query CCDS DB by CCDS ID:42751.2Re-query CCDS DB by GeneID:55627See the combined annotation on chromosome 2 in Sequence Viewer

Public Note for CCDS 42751.1
This CCDS representation uses the 5'-most in-frame start codon. While this start codon is well-conserved, it should be noted that other than human and chimp, all other species have indels that follow this start codon. Other primates and rodents have frameshifting indels, and thus cannot use this start codon. However, some mammalian species, including cow, pig and dog, contain additional compensating indels that bring them back in frame; these species could therefore use the start codon represented in this CCDS. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 39 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.

Public since: CCDS release 5, NCBI annotation release 36.3, Ensembl annotation release 47

Review status: Reviewed (by RefSeq, Havana and CCDS collaboration)


Attributes
CDS uses downstream AUG

Sequence IDs included in CCDS 42751.2

Original Current Source Nucleotide ID Protein ID MANE Status in CCDS Seq. Status Links
Original member Current member EBI ENST00000680298.1 ENSP00000506463.1 MANE Select Accepted alive Link to Ensembl Transcript Viewer:ENST00000680298.1Link to Ensembl Protein Viewer:ENSP00000506463.1Re-query CCDS DB by Nucleotide ID:ENST00000680298Re-query CCDS DB by Protein ID:ENSP00000506463
Original member Current member NCBI NM_017951.5 NP_060421.3 MANE Select Accepted alive Link to Nucleotide Sequence:NM_017951.5Link to Protein Sequence:NP_060421.3Re-query CCDS DB by Nucleotide ID:NM_017951Re-query CCDS DB by Protein ID:NP_060421Link to BLAST:NP_060421.3

Chromosomal Locations for CCDS 42751.2

Assembly GRCh38.p14 (GCF_000001405.40)

On '-' strand of Chromosome 2 (NC_000002.12)
Genome Browser links: Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2See the combined annotation on chromosome 2 in Sequence Viewer

Chromosome Start Stop Links
2 130152555 130152884 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130153043 130153171 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130153319 130153450 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130153702 130153935 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130154277 130154482 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130155096 130155259 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130156035 130156135 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130156585 130156675 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130157251 130157396 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130161186 130161272 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130164374 130164445 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130167458 130167590 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130172349 130172500 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130172625 130172677 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130172787 130172895 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130173279 130173354 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130173514 130173656 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130174914 130175000 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2
2 130176554 130176592 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 2Link to Ensembl Genome Browser on chromosome 2

CCDS Sequence Data
Blue highlighting indicates alternating exons.
Red highlighting indicates amino acids encoded across a splice junction.
 
Mouse over the nucleotide or protein sequence below and click on the highlighted codon or residue to select the pair.

Nucleotide Sequence (2484 nt):
ATGGCGTTCCCTCACCTGCAGCAGCCCAGCTTTCTACTGGCTAGCCTGAAAGCTGACTCTATAAATAAGC
CCTTTGCACAGCAGTGCCAAGACTTGGTTAAAGTCATTGAGGACTTTCCAGCAAAGGAGCTGCACACCAT
CTTCCCATGGCTGGTAGAAAGCATTTTTGGCAGCCTAGATGGTGTCCTCGTTGGCTGGAACCTCCGCTGC
TTACAGGGGCGCGTGAATCCTGTGGAGTACAGCATCGTGATGGAATTTCTCGACCCTGGTGGCCCAATGA
TGAAGTTGGTTTATAAGCTTCAAGCTGAAGACTATAAGTTCGACTTTCCTGTCTCCTACTTGCCTGGTCC
TGTGAAGGCGTCCATCCAGGAGTGCATCCTCCCTGACAGTCCTCTGTACCACAACAAGGTCCAGTTCACC
CCTACTGGGGGCCTTGGTCTGAACTTGGCCCTGAATCCGTTCGAGTATTACATATTCTTCTTTGCCTTGA
GCCTCATCACTCAGAAGCCACTTCCTGTGTCCCTCCACGTCCGTACTTCAGACTGTGCCTATTTCATCCT
GGTGGACAGGTACCTGTCATGGTTCCTGCCCACCGAAGGCAGTGTGCCCCCACCACTCTCCTCCAGCCCA
GGGGGGACCAGCCCCTCACCACCTCCCAGGACACCAGCCATACCCTTTGCTTCCTATGGCCTCCACCACA
CTAGCCTCCTAAAGCGACACATCTCTCATCAGACGTCTGTGAATGCAGACCCCGCCTCCCACGAGATCTG
GAGGTCAGAAACTCTGCTCCAGGTTTTTGTTGAAATGTGGCTTCATCACTATTCCTTGGAGATGTATCAA
AAAATGCAGTCCCCTCATGCCAAGCTGGAGGTTCTGCACTACCGACTCAGTGTCTCCAGCGCCCTCTACA
GCCCCGCCCAACCCAGCCTCCAGGCCCTCCACGCCTACCAAGAGTCGTTCACGCCTACTGAGGAGCATGT
GTTGGTGGTGCGCCTGCTGCTGAAGCACCTGCACGCCTTTGCCAACAGCCTGAAGCCAGAGCAGGCCTCA
CCCTCCGCCCACTCCCACGCCACCAGCCCCCTGGAGGAGTTCAAACGGGCTGCTGTCCCGAGGTTCGTCC
AGCAGAAACTCTACCTCTTCTTGCAGCATTGCTTTGGCCACTGGCCCCTGGACGCATCGTTCAGAGCTGT
CCTGGAGATGTGGCTGAGCTACCTGCAGCCGTGGCGGTACGCGCCTGACAAGCAGGCTCCGGGCAGCGAC
TCCCAGCCCCGGTGTGTGTCGGAGAAATGGGCACCCTTTGTCCAGGAGAACCTGCTGATGTACACCAAGT
TGTTTGTGGGCTTTCTGAACCGCGCGCTCCGCACAGACCTGGTCAGCCCCAAGCACGCGCTCATGGTGTT
CCGAGTGGCCAAAGTCTTTGCCCAGCCCAACCTGGCTGAGATGATTCAGAAAGGTGAGCAGCTATTCCTG
GAGCCAGAGCTGGTCATCCCCCACCGCCAGCACCGACTCTTCACGGCCCCCACATTCACTGGGAGCTTCC
TGTCACCCTGGCCACCAGCGGTCACTGATGCCTCCTTCAAGGTGAAGAGCCACGTCTACAGCCTGGAGGG
CCAGGACTGCAAGTACACCCCGATGTTTGGGCCCGAGGCCCGCACCCTGGTCCTGCGCCTCGCTCAGCTC
ATCACACAGGCCAAACACACAGCCAAGTCCATCTCCGACCAGTGTGCGGAGAGCCCGGCTGGCCACTCCT
TCCTCTCATGGCTGGGCTTTAGCTCCATGGACACCAATGGCTCCTACACAGCCAACGACCTGGACGAGAT
GGGGCAAGACAGTGTCCGGAAGACAGATGAATACCTGGAGAAGGCCCTGGAGTACCTGCGCCAGATATTC
CGGCTCAGCGAAGCGCAGCTCAGGCAGTTCACACTCGCCTTGGGCACCACCCAGGATGAGAATGGAAAAA
AGCAACTCCCCGACTGCATCGTGGGTGAGGACGGACTCATCCTTACGCCCCTGGGGCGGTACCAGATCAT
CAATGGGCTGCGAAGGTTTGAAATTGAGTACCAGGGGGACCCGGAGCTGCAGCCCATCCGGAGCTATGAG
ATCGCCAGCTTGGTCCGCACACTCTTTAGGCTGTCGTCTGCCATCAACCACAGATTTGCAGGACAGATGG
CGGCTCTGTGTTCCCGGGATGACTTCCTCGGCAGCTTCTGTCGCTACCACCTCACAGAACCTGGGCTGGC
CAGCAGGCACCTGCTGAGCCCTGTGGGGCGGAGGCAGGTGGCCGGCCACACCCGCGGCCCCAGGCTCAGC
CTGCGCTTCCTGGGCAGTTACCGGACGCTGGTCTCGCTGCTGCTGGCCTTCTTCGTGGCCTCTCTGTTCT
GCGTCGGGCCCCTCCCATGCACGCTGCTGCTCACCCTGGGCTATGTCCTCTACGCCTCTGCCATGACACT
GCTGACCGAGCGGGGGAAGCTGCACCAGCCCTGA

Translation (827 aa):
MAFPHLQQPSFLLASLKADSINKPFAQQCQDLVKVIEDFPAKELHTIFPWLVESIFGSLDGVLVGWNLRC
LQGRVNPVEYSIVMEFLDPGGPMMKLVYKLQAEDYKFDFPVSYLPGPVKASIQECILPDSPLYHNKVQFT
PTGGLGLNLALNPFEYYIFFFALSLITQKPLPVSLHVRTSDCAYFILVDRYLSWFLPTEGSVPPPLSSSP
GGTSPSPPPRTPAIPFASYGLHHTSLLKRHISHQTSVNADPASHEIWRSETLLQVFVEMWLHHYSLEMYQ
KMQSPHAKLEVLHYRLSVSSALYSPAQPSLQALHAYQESFTPTEEHVLVVRLLLKHLHAFANSLKPEQAS
PSAHSHATSPLEEFKRAAVPRFVQQKLYLFLQHCFGHWPLDASFRAVLEMWLSYLQPWRYAPDKQAPGSD
SQPRCVSEKWAPFVQENLLMYTKLFVGFLNRALRTDLVSPKHALMVFRVAKVFAQPNLAEMIQKGEQLFL
EPELVIPHRQHRLFTAPTFTGSFLSPWPPAVTDASFKVKSHVYSLEGQDCKYTPMFGPEARTLVLRLAQL
ITQAKHTAKSISDQCAESPAGHSFLSWLGFSSMDTNGSYTANDLDEMGQDSVRKTDEYLEKALEYLRQIF
RLSEAQLRQFTLALGTTQDENGKKQLPDCIVGEDGLILTPLGRYQIINGLRRFEIEYQGDPELQPIRSYE
IASLVRTLFRLSSAINHRFAGQMAALCSRDDFLGSFCRYHLTEPGLASRHLLSPVGRRQVAGHTRGPRLS
LRFLGSYRTLVSLLLAFFVASLFCVGPLPCTLLLTLGYVLYASAMTLLTERGKLHQP


Links Key
 Links to:   History report
  BLAST report
  Entrez Gene
  Nucleotide report
  Protein report
 Re-query CCDS DB by:   CCDS ID
  Gene ID
  Nucleotide ID
  Protein ID
 Genome Browser Links:   Ensembl Genome Browser
  NCBI Sequence Viewer
  UCSC Genome Browser
  VEGA Genome Browser

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