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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 History](IMG/ccds-History.jpg) ![](/corehtml/transparent.gif) ![NCBI Gene:55627](IMG/ccds-Gene.jpg) ![](/corehtml/transparent.gif) ![Re-query CCDS DB by CCDS ID:42751.2](IMG/ccds-Cquery.jpg) ![](/corehtml/transparent.gif) ![Re-query CCDS DB by GeneID:55627](IMG/ccds-Gquery.jpg) ![](/corehtml/transparent.gif) ![See the combined annotation on chromosome 2 in Sequence Viewer](IMG/ccds-SeqViewer.jpg) ![](/corehtml/transparent.gif) |
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](IMG/ccds-Check.jpg) |
![Current member](IMG/ccds-Check.jpg) |
EBI |
ENST00000680298.1 |
ENSP00000506463.1 |
MANE Select |
Accepted |
alive |
![Link to Ensembl Transcript Viewer:ENST00000680298.1](IMG/ccds-Nucleotide.jpg) ![Link to Ensembl Protein Viewer:ENSP00000506463.1](IMG/ccds-Protein.jpg) ![](/corehtml/transparent.gif) ![Re-query CCDS DB by Nucleotide ID:ENST00000680298](IMG/ccds-Nquery.jpg) ![Re-query CCDS DB by Protein ID:ENSP00000506463](IMG/ccds-Pquery.jpg) ![](/corehtml/transparent.gif) |
![Original member](IMG/ccds-Check.jpg) |
![Current member](IMG/ccds-Check.jpg) |
NCBI |
NM_017951.5 |
NP_060421.3 |
MANE Select |
Accepted |
alive |
![Link to Nucleotide Sequence:NM_017951.5](IMG/ccds-Nucleotide.jpg) ![Link to Protein Sequence:NP_060421.3](IMG/ccds-Protein.jpg) ![](/corehtml/transparent.gif) ![Re-query CCDS DB by Nucleotide ID:NM_017951](IMG/ccds-Nquery.jpg) ![Re-query CCDS DB by Protein ID:NP_060421](IMG/ccds-Pquery.jpg) ![](/corehtml/transparent.gif) ![Link to BLAST:NP_060421.3](IMG/ccds-BLAST.jpg) ![](/corehtml/transparent.gif) |
Chromosomal Locations for CCDS 42751.2
Assembly GRCh38.p14 (GCF_000001405.40)
CCDS Sequence Data |
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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
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