RetrogeneDB ID: retro_pmar_9

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL499373:76..994(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000010298
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gapdhs (1 of 2)
• Ensembl ID: ENSPMAG00000009321
• Aliases: None
• Description: glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [Source:ZFIN;Acc:ZDB-GENE-020913-1]

Sequence

>retro_pmar_9
ATGGTGAACATCGGCATCAATGGGTTTGGCCGTATTGGCCGTCTGGTGGCTCGTGCTGCCGTGCAAAAGGAAGACATTAA
TGTGGTGGCCATCAACGACCCCTTCATTGACCTGGAGTACATGGTCTACATGTTCAAGTATGACTCTACCCATGGACGAT
TCAAGGGAGACGTGAAGGTTGAGGATGGGAAGCTGTTGATCAATGGACATGCCGTTTCCGTCTACTCGGAGCGTGACCCC
GCCAACATCCCATGGGGTAAGCATGGTGCCGATTACGTGGTGGAGTCCACCGGTGTGTTCACCACCATCGATAAGGCCTC
TTTGCACCTGAAGGGCGGTGCAAAGCACGTCATCATCTCGGCCCCGTCTGCGGATGCGCCAATGTTCGTGATGGGAGTAA
ACCACGAGAAGTACGACCCCTCGCTGAAGGTGGTCAGCAACGCGTCGTGCACTACCAACTGCCTGGCTCCTCTGGCCAAG
GTCATCAACGACAACTTCGGCATCGTGGAGGGGCTCATGACCACGGTGCACTCGTACACGGCAACGCAGAAGACTGTGGA
CGGGCCTTCTGCAAAGTTGTGGCGTGACGGCCGCGGGGCTTCTCAGAACATCATCCCGGCCTCGACTGGCGCTGCCAAGG
CCGTGGGGATGGTCATCCCCGAGCTCAACGGAAAGCTGACCGGCATGGCGTTCCGCGTGCCGACTCCCAACGTCTCGGTG
GTCGACCTCACGTGCCGTCTGGCCAAGCCGGCCTCGTATGATGAAATCAAGGCCAAGGTTCGCGAGGCATCCAAGGGTGA
CCTGAAGGGAATCCTGGGATACACCGAGGATTTGGTCGTGTCCACCGACTTCAATGGCGACACCCACTCGTCCATCTTCG
ACGCACAAGCTGGCATCGCTCTCAACAAGCAGTTCGTC

Alignment

ORF - retro_pmar_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IISIGIINQFGRIGRLVARAAVQKEDINVVAINDPFIDLEYMVYMFKYDSTHGRFKGDVKVEDGKLLING
          ...IGI.N.FGRIGRLVARAAVQKEDINVVAINDPFIDLEYMVYMFKYDSTHGRFKGDVKVEDGKLLING
Retrocopy MVNIGI-NGFGRIGRLVARAAVQKEDINVVAINDPFIDLEYMVYMFKYDSTHGRFKGDVKVEDGKLLING

Parental  HAVSVYSERDPANIPWGKHGADYVVESTGVFTTIDKASLHLKGGAKHVIISAPSADAPMFVMGVNHEKYD
          HAVSVYSERDPANIPWGKHGADYVVESTGVFTTIDKASLHLKGGAKHVIISAPSADAPMFVMGVNHEKYD
Retrocopy HAVSVYSERDPANIPWGKHGADYVVESTGVFTTIDKASLHLKGGAKHVIISAPSADAPMFVMGVNHEKYD

Parental  PSLKVVSNASCTTNCLAPLAKVINDNFGIVEGLMTTVHSYTATQKTVDGPSAKLWRDGRGASQNIIPAST
          PSLKVVSNASCTTNCLAPLAKVINDNFGIVEGLMTTVHSYTATQKTVDGPSAKLWRDGRGASQNIIPAST
Retrocopy PSLKVVSNASCTTNCLAPLAKVINDNFGIVEGLMTTVHSYTATQKTVDGPSAKLWRDGRGASQNIIPAST

Parental  GAAKAVGMVIPELNGKLTGMAFRVPTPNVSVVDLTCRLAKPVTRD
          GAAKAVGMVIPELNGKLTGMAFRVPTPNVSVVDLTCRLAKP...D
Retrocopy GAAKAVGMVIPELNGKLTGMAFRVPTPNVSVVDLTCRLAKPASYD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Petromyzon marinus was not studied using RNA-Seq expression data.

ChIP-Seq

Petromyzon marinus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_pmar_9 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CO552581	194	488	100	294	0	294
DY249702	290	663	100	373	0	373
EE742837	110	371	100	237	0	236

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_9 was not experimentally validated.

Homology

Retrocopy orthology:

Petromyzon marinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000061099	2 retrocopies	retro_mmus_3024, retro_mmus_528,
Otolemur garnettii	ENSOGAG00000009491	25 retrocopies	retro_ogar_1269, retro_ogar_1332, retro_ogar_1460, retro_ogar_1472, retro_ogar_1798, retro_ogar_1968, retro_ogar_2074, retro_ogar_2266, retro_ogar_2376, retro_ogar_2446, retro_ogar_2469, retro_ogar_2631, retro_ogar_2647, retro_ogar_2884, retro_ogar_2957, retro_ogar_315, retro_ogar_3197, retro_ogar_3262, retro_ogar_3517, retro_ogar_355, retro_ogar_468, retro_ogar_582, retro_ogar_632, retro_ogar_658, retro_ogar_785,
Petromyzon marinus	ENSPMAG00000009321	1 retrocopy	retro_pmar_9 ,
Pan troglodytes	ENSPTRG00000010848	1 retrocopy	retro_ptro_2211,
Tupaia belangeri	ENSTBEG00000008617	16 retrocopies	retro_tbel_1017, retro_tbel_1193, retro_tbel_124, retro_tbel_1650, retro_tbel_1685, retro_tbel_2010, retro_tbel_2486, retro_tbel_249, retro_tbel_2793, retro_tbel_2832, retro_tbel_2873, retro_tbel_2929, retro_tbel_3117, retro_tbel_425, retro_tbel_4292, retro_tbel_4346,