RetrogeneDB ID: retro_pmar_3

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL484525:3948..4953(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000010333
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RDH13
• Ensembl ID: ENSPMAG00000009095
• Aliases: None
• Description: retinol dehydrogenase 13 (all-trans/9-cis) [Source:HGNC Symbol;Acc:19978]

Sequence

>retro_pmar_3
CCCGTCGAGTTGACGCGGGACATGGGTCCTGGCATCCAGGCGCTGGCCGGCACCGCGGGTTGCGGCCTCCTGCTGCTTGT
GGTCCTCCTCGCCGCGGCGCGCCGCCGCCTGCACGGGCGGCCCTCGCCGCTGGCCCTCGCGGCCTGCAGCATGCGCGGCA
AGACCGTGGTGGTCACGGGGGCCAACTGCGGCCTGGGCCGCGCCACGACGTTGGCGCTCGCCCGCCTCGGGGCCCGCGTC
ATCCTGGCCGTGCGCGACTCGGCGCGGGGCGAGGAGGCGGCGGTGGAGCTCCGTCGGGAGCTGGGCTCCGAGGAGGCCGA
GCTGGTGGTGCGCGAGCTCGACCTCGCGTCCCTGGCGTCCGTGCGCCGCTTCTGCGCGCGGTTGGAGCGCGAGGAGGAGC
GGCTGGACGTGCTGGTGAACAACGCCGGGGTGTTCCGCTGCCCCTACGCGCTCACCGAGGACGGCTTCGAGACGCAGTTC
GGAGTCAACCACCTGGGCCACTTCCTCCTCACCGCGCTGCTGCTGCCGCTGCTGGGCCGCTCGGCGCCCAGCCGCGTCGT
GGTCGTGTCCTCGGCCCTCTACAAGCAGGGCCGCATCAACTTCGACGACCTGGCGAGCGAGCGCTCCTACGACCCCGCGG
CCGCGTACGGCCGCAGCAAGTTGGCCAACGTGATGTTCGCGCGCGAGCTGGCGCGGCGCCTGCGTGGCCAGGGCGTCACG
GCCAACGCGCTGCACCCGGGCGTCGTGCGCACCAACCTGGGCCGCCACGTCTCCATGCCGGCCCTGGCCCGGCCGCTCTT
CAACCTCCTCGCCTGGGCCGCTTTCCGCACCCCCGAGCAGGGCGCTCGTACGGCCGTCTTCCTCGCAGCCTCGCCCGACG
TGGCGGACGTCAGCGGCGCCTACTTCGGCGACTGCCGCCAGGAGGAGCTCCTGCCCGTAGCCACGGACGACGCCGTGGCC
GCCAAATTGTGGGAGGTCAGCGAGCGCCTGGTGGGCCTGCGCTCT

Alignment

ORF - retro_pmar_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.09 %
• Parental protein coverage: 81.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CWVGFEGACVLAVRAGARVILACRDEAACEDAAREIR---GETLNPRVARRLDLASLESVRDFAAHINQD
          C..G......LA.R.GARVILA.RD.A..E.AA.E.R...G......V.R.LDLASL.SVR.F.A.....
Retrocopy CGLGRATTLALA-RLGARVILAVRDSARGEEAAVELRRELGSEEAELVVRELDLASLASVRRFCARLERE

Parental  EENVHILVNNAAVMRCPHSTTADGFEMQFGVNHLGHFLLTNLLLDKLRASAPSRVVTVSSLAQVAACLDL
          EE....LVNNA.V.RCP...T.DGFE.QFGVNHLGHFLLT.LLL..L..SAPSRVV.VSS..........
Retrocopy EERLDVLVNNAGVFRCPYALTEDGFETQFGVNHLGHFLLTALLLPLLGRSAPSRVVVVSSALYKQGRINF

Parental  SDLNWERRKYDPKLAYCDSKLANVLFSLELSKRLQGTGVTANSVNPGVCNTSLGRHTGMHKSAFSSSVLG
          .DL..E.R.YDP..AY..SKLANV.F..EL..RL.G.GVTAN...PGV..T.LGRH..M...A.......
Retrocopy DDLASE-RSYDPAAAYGRSKLANVMFARELARRLRGQGVTANALHPGVVRTNLGRHVSM--PALARPLFN

Parental  PFFWLVVRSPRLGAQPSINLAVSEELRDVSGRYFDGMRQVDPGTKANDEELARQLWEASARLVCLR
          ...W...R.P..GA.....LA.S....DVSG.YF...RQ......A.D...A..LWE.S.RLV.LR
Retrocopy LLAWAAFRTPEQGARTAVFLAASPDVADVSGAYFGDCRQEELLPVATDDAVAAKLWEVSERLVGLR

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

No EST(s) were mapped for retro_pmar_3 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_3 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003306	1 retrocopy	retro_amel_114,
Equus caballus	ENSECAG00000023146	1 retrocopy	retro_ecab_338,
Ochotona princeps	ENSOPRG00000015998	2 retrocopies	retro_opri_286, retro_opri_524,
Petromyzon marinus	ENSPMAG00000009095	1 retrocopy	retro_pmar_3 ,
Pongo abelii	ENSPPYG00000010398	1 retrocopy	retro_pabe_1972,
Pan troglodytes	ENSPTRG00000011484	1 retrocopy	retro_ptro_1576,
Sorex araneus	ENSSARG00000003600	1 retrocopy	retro_sara_314,
Tupaia belangeri	ENSTBEG00000016531	1 retrocopy	retro_tbel_1570,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,