RetrogeneDB ID: retro_xmac_22

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556698.1:1510677..1511586(-)
• Located in intron of: ENSXMAG00000013408

Retrocopy information

• Ensembl ID: ENSXMAG00000019519
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: atp1b1a
• Ensembl ID: ENSXMAG00000016407
• Aliases: None
• Description: ATPase, Na+/K+ transporting, beta 1a polypeptide [Source:ZFIN;Acc:ZDB-GENE-001127-3]

Sequence

>retro_xmac_22
TGTGGAGCCAACATGTCTGGAGGAAAGAGCGGCGGATGGAGGGAAACCTTATGGGATCCAGAGAAGAGAGAGTTTCTAGG
GCGAACAGGGGACAGTTGGCTTAAGATATCCGTGTTCTACGTGATTTTCTACGCATTCCTGTGTGGGATTTTCGTCGCGA
CCATTCTGGTTTTGCTGATGACTTTAAATATGTACAAACCCAAATACCAGGACAGAATTCTTCCCTCAGGTCTGTCATTC
TCACCCTACGCCCACAACCTTGAGATCATTTACAAGACGGACGACCCGTCTTCATATGAGGTGTACGTCAAAAACCTGAA
GGAGTTTATTGAGCAATATAATGATGAGAAACAGACCGACGACATGAAATATGAGGATTGTGGAACCACCCCGAAGTTAT
ACACTGAACGCGGCGAACTCGAAAGTAATACAGGACAGAGGAAAAGTTGCCGCTTCAGCAGAAGGGAGCTTCAAGGCTGC
TCTGGGGAAAACGACACCACCTTTGGCTTTAAGGAGGGAAAGCCGTGCCTCATTGTCAAGCTCAACAGGATTATCAATTT
CAGACCAAAACCTCCTTCCAGCAGCGATTTGCTTCCAGACGATCTGCAAGGCAAATCCTTTTATAACTTCCTCCCCGTTC
ACTGCACGAATAGATGGGCGGAAGACGACGGCCTGATCGGAGAGATCAAGTACTTTGGCTTCGCGGGCAACGCCGGTTTC
CCTCTCCAGTACTTCCCCTACTACGGCAAAATGCTGCATCCCAATTACCTGCAGCCTCTGGTGGGCATCAAGTTCACCAA
CCTCACCAAGAACAGGGAGCTCCGCATCAAGTGCAAAGTGTACGGGGAAGGCTACACGGCGGAAGGCATTGATGGACTAT
TTTACGTTCGCGTCACTGTGAAACAGTGA

Alignment

ORF - retro_xmac_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.04 %
• Parental protein coverage: 96.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGWRKFLWNSEKREFLGRTGGSWLKIFLFYVIFYGCLAAIFIGTIQALLLTIHEFKPTHQDRVAPPGLSH
          GGWR..LW..EKREFLGRTG.SWLKI..FYVIFY..L..IF..TI..LL.T....KP..QDR..P.GLS.
Retrocopy GGWRETLWDPEKREFLGRTGDSWLKISVFYVIFYAFLCGIFVATILVLLMTLNMYKPKYQDRILPSGLSF

Parental  TPRSDKSEISFKISDPASYQRYTASMMAFLKPYSKEEQDKDSNYEDCSESPKTYTDRGKLEDDHGVRKSC
          .P.....EI..K..DP.SY..Y......F...Y..E.Q..D..YEDC...PK.YT.RG.LE...G.RKSC
Retrocopy SPYAHNLEIIYKTDDPSSYEVYVKNLKEFIEQYNDEKQTDDMKYEDCGTTPKLYTERGELESNTGQRKSC

Parental  YFYRSHLGSCSGETDESFGFSEGKPCLIVKLNRIVNFRPKPPTNNSTLPDGLKGKTFENYIPIHCKNRRE
          .F.R..L..CSGE.D..FGF.EGKPCLIVKLNRI.NFRPKPP.....LPD.L.GK.F.N..P.HC.NR..
Retrocopy RFSRRELQGCSGENDTTFGFKEGKPCLIVKLNRIINFRPKPPSSSDLLPDDLQGKSFYNFLPVHCTNRWA

Parental  EDESKIGEIKYFGLGGLAGFPLQYYPYYGKRLHPNYLQPLVAIQFTNLTLKEELRIECKVYGDNIDYNEK
          ED...IGEIKYFG..G.AGFPLQY.PYYGK.LHPNYLQPLV.I.FTNLT...ELRI.CKVYG........
Retrocopy EDDGLIGEIKYFGFAGNAGFPLQYFPYYGKMLHPNYLQPLVGIKFTNLTKNRELRIKCKVYGEGYTAEGI

Parental  DRYQGRFDVKFTV
          D...G.F.V..TV
Retrocopy D---GLFYVRVTV

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_22 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_22 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010317	1 retrocopy	retro_cjac_2288,
Homo sapiens	ENSG00000143153	1 retrocopy	retro_hsap_2924,
Gorilla gorilla	ENSGGOG00000002499	1 retrocopy	retro_ggor_2027,
Pan troglodytes	ENSPTRG00000001653	1 retrocopy	retro_ptro_1979,
Xiphophorus maculatus	ENSXMAG00000016407	1 retrocopy	retro_xmac_22 ,