RetrogeneDB ID: retro_xmac_7

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH558508.1:1464..2805(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019994
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OPN4 (2 of 3)
• Ensembl ID: ENSXMAG00000015929
• Aliases: None
• Description: opsin 4 [Source:HGNC Symbol;Acc:14449]

Sequence

>retro_xmac_7
ATGGCCGGAAACTGCACAGATCACCAGAAACACCTGGGGATGCCCGTCCCCACCCACGGCGCCCTGCAGCAGCAGCGCCC
GTTCCCTACTGTGGACGTTCCTGCGCATGCCCATTACATCATCGGCTGTGTGATCCTGTTGGTGGGAGTGATGGGCACGC
TGGGGAACGCTCTGGTCATCTACGTGTTCTGTCGTAGCAAGACGCTGCGGACACCCAGCAACCTGCTGGTGGTCAACCTG
GCGCTGGCGGACTTCCTGATGTCGGTGACGCAATCTCCGGTCTTCTTCGTGGCCAGCCTGCACCGCCGCTGGGTGTTCGG
AGAGTTTGCCTGCGAGCTCTATGCCTTCTGCGGCGCTCTGTTCGGCATCGCGTCCATGATGACGCTCACGGCCATCGCCG
GGGACCGCTGCCTGGCCATCACGCGGCCGCTGGCGCTGCTGGGCGCCGTGAGCCGCCAGCGGCTCTCCGTGGTGGCCGTG
GGGCTGTGGGTGTACTCGCTGGGCTGGAGTCTGCCGCCGTTCTTTGGGTGGAGTGCCTACGTCCCTGAAGGTCTACAGAC
GTCCTGCAGCTGGGATTACATGAGCTTCACGGTCACGGTGCGCACCTACACCGTCCTGCTCTTCGTCTTCGTCTTCTTCA
TCCCCCTGGCCGTCATCGGCTCCTGCTACCTGGCCATCTTCAGGGCCGTGCGACGGGCGGCTCAGGAGGTGAAGAGGCTG
AGCAGTGGCGAGACCACCAAGGCGTATGAACGGCTGCGCGGCGAGTGGCGGATGGCCCGAGTGGCTCTGGGAGTCATTCT
GCTCTTCGTCGTGTCCTGGTCGCCGTACTCCGCCGTCGCCCTGACCGCCACCGCTGGCTACGCCCACCTGCTGACCCCCT
ACATGAACTCGGTACCTGCAATCATCGCCAAGGCCTCCGCCATCCACAACCCCATCATCTACGCCATCACACATCCAAAG
TATCGTGCTGCCATTGGTCGACACTTCCCGCTGCTGCGTGCTGTGCTGCGGCTGCATGAAAAGGACCTTCAGTCCCCGTT
CAGCTCCAGCACCGCCTCGTCTCGCCGCACCACGCTCAGCGGTTCGCCAGGGGTCCGGCTGGGCGCTGGGGTCCGCTGGC
CGCAGAGCCGGCTGTCCTCAGCTTCTGACAGCGACTCCTGCTGGACGGAAAGCGAAGCTGACGGCTCCAGCGCCGCATCA
ACAGCCATCAACCGCCGGACATCCACCCAGGTGTCAGCTGAGCCGTCTGACCCCGCCCACATGAGCCATCGGGTTGAGTC
TAGACCGACAGACAGCGACTCACCTGAAGGGGGCGCTGCCATGGCGGCAAAACTTCTGCTG

Alignment

ORF - retro_xmac_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.4 %
• Parental protein coverage: 74.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIVPAHAFPTVNVPAHAHYTIGVVILAVGITGMLGNFLVIYAFCRSRSLRTPSNIFIINLAVTDFLMCLT
          A......FPTV.VPAHAHY.IG.VIL.VG..G.LGN.LVIY.FCRS..LRTPSN....NLA..DFLM..T
Retrocopy ALQQQRPFPTVDVPAHAHYIIGCVILLVGVMGTLGNALVIYVFCRSKTLRTPSNLLVVNLALADFLMSVT

Parental  QTPIFFITSMHKHWIFGKKGCELYAFCGALFGICSMMTLMVIAVDRYVVITRPLASLGVMSHRKALCFVA
          Q.P.FF..S.H..W.FG...CELYAFCGALFGI.SMMTL..IA.DR...ITRPLA.LG..S.........
Retrocopy QSPVFFVASLHRRWVFGEFACELYAFCGALFGIASMMTLTAIAGDRCLAITRPLALLGAVSRQRLSVVAV

Parental  AAWVYSTGWSLPPFFGWSAYVPEGLMTSCSWDYMTFTPSVRSYTMLLFTFVFFIPLFIIIFCYCGIFRAI
          ..WVYS.GWSLPPFFGWSAYVPEGL.TSCSWDYM.FT..VR.YT.LLF.FVFFIPL..I..CY..IFRA.
Retrocopy GLWVYSLGWSLPPFFGWSAYVPEGLQTSCSWDYMSFTVTVRTYTVLLFVFVFFIPLAVIGSCYLAIFRAV

Parental  RHTTRAITKINCEGRRDSAKRFHKMRSEWKMAKIALIVILLFVISWAPYSCAALTAFAGYADLLTPYMNS
          R..................K.....R.EW.MA..AL.VILLFV.SW.PYS..ALTA.AGYA.LLTPYMNS
Retrocopy RRAAQEVKRLS---SGETTKAYERLRGEWRMARVALGVILLFVVSWSPYSAVALTATAGYAHLLTPYMNS

Parental  VPAVIAKASAIHNPIIYAITHPKYRSAISRYVPYLGMLLCISGRDRYS--SSSLQSTRRSTLTSQSECK-
          VPA.IAKASAIHNPIIYAITHPKYR.AI.R..P.L...L.....D..S..SSS..S.RR.TL........
Retrocopy VPAIIAKASAIHNPIIYAITHPKYRAAIGRHFPLLRAVLRLHEKDLQSPFSSSTASSRRTTLSGSPGVRL

Parental  GTG-RHHTSSQSESESAHLSDTEEDCSSRTPAGRLLSAEVRHASQRSKVSGHSAGASERTAALNPTD
          G.G.R...S..S.........TE........A........R...Q.S......A..S.R.....PTD
Retrocopy GAGVRWPQSRLSSASDSDSCWTESEADGSSAASTAINR--RTSTQVSAEPSDPAHMSHRVES-RPTD

Legend:

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

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_7 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_7 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000022098	1 retrocopy	retro_drer_8,
Oreochromis niloticus	ENSONIG00000015868	1 retrocopy	retro_onil_10,
Xiphophorus maculatus	ENSXMAG00000015929	1 retrocopy	retro_xmac_7 ,
Xiphophorus maculatus	ENSXMAG00000017297	1 retrocopy	retro_xmac_11,