RetrogeneDB ID: retro_xmac_15

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556875.1:785668..786883(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019967
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXMAG00000003895
• Aliases: None
• Description: None

Sequence

>retro_xmac_15
ATGGAGAATGGCGTCAGACCAGCAGAAAACAGGAGATGTTTTGGCTTCTCACGGCGCCACAGCCTTTTCTTACTTCTGGT
TCTCGCAGTTGTGCTTTTTGTCTACTGTACCAACATCCGGGACAAGGGGCACGAGTGGAACCCCAAAGAGTGGATGAACA
GTCATTCAATGAAACTACTCACTGTGTTCACAAAACAAAGCACCGTCTCCAAAAACACAGGATTTACAGATGCAAACACC
ACTGCTGAACTTCCTGAAACTACGAGCGTCGCCACAACGCAGGAGCCACCGACTCAACGGCAGAGGACAGTTTCATCACG
GGTCACCAAGAAGGTGCTAGAAACCCAGACTGCCCAACGGACAGCGGCTCCTTATGTGTCTCCTGGACCGTACTTGGTGG
AGTACCCCTATGAGTACCACTTTACTATCAATGAGGAACTGAAATGTAGGCAGGAGAAGCCGTTTGTGGTTCTGATCGTA
CAAGTGGCGCCACGCAACCGAGCTCATCGCGACATCATCCGTAACAGCTGGGGAAGCGAGAAGCTGGCTAACAACCAAGT
GGTGGCGCTGTTCTTCCTGCTGGGGATGCAGACTGGAGACGATGCAGAGCAGGTCCACCGGCAGCTGCTGCAGGAGAGCA
AAGAGCATCAGGACCTGATCCAGGGAGACTTTGTGGACTGCTACAAGAACCTGACCATAAAGACCATGGTGATGCTGGAG
TGGCTGAACTCCTACTGCTCCAGCGCCGCTTACGCCATGAAAATCGATTCAGACATGTTTCTAAATGTTCCCAATCTGGT
CAACTTGCTCCTCAAAGCTCCAAGGACAAACTACATGACCGGCCTGGTGGCACATGGAGCAGCTGTCTTGAGGGATCCCA
ACTCCAAATGGTACTTACCTCGTGAAATTTTGAGCGAAGATGTTTACCCTCCCTATGCTTTGGGTCTGGGCTACATTTTG
TCTTTGGATCTCACCAAAAAGCTCATTGAGGCTTCCAGACACGTTAAACCTCTTTATATTGAAGATGTATATTTGGGCTT
ATGTATGAGACACCTGGGTATCCGTCCAACAGAACCTCCGAGTTACTCCTTCCACGTTTTTCCTGTGAGATACAGTCGCT
GTGAATACTCCAAGATTATCGCAACCACAACTCTTCAAAATATGGACCGTGTTTGGATTTGGAGAGACTTTAAGAAACCG
GGTCGGTACTGTTGA

Alignment

ORF - retro_xmac_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.29 %
• Parental protein coverage: 86.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSLAQREDSSSDDNKM----TVKSISPSHSIPSQFYVEYPYRYHFILDEPTRCRQESPFVVVMIPVAPQG
          P...QR..SS....K.....T..........P....VEYPY.YHF...E...CRQE.PFVV....VAP..
Retrocopy PTQRQRTVSSRVTKKVLETQTAQRTAAPYVSPGPYLVEYPYEYHFTINEELKCRQEKPFVVLIVQVAPRN

Parental  REARDIIRRTWGRESQVLGQLISYYFLLGKSRIGNDAEPPEEQILNESKKYHDILQSNFLDSYKNLTIKT
          R..RDIIR..WG.E.....Q.....FLLG....G.DAE....Q.L.ESK...D..Q..F.D.YKNLTIKT
Retrocopy RAHRDIIRNSWGSEKLANNQVVALFFLLGM-QTGDDAEQVHRQLLQESKEHQDLIQGDFVDCYKNLTIKT

Parental  MVMLEWLGSHCPNTSYAMKVDSDTFLNVRNLVDLLLEAPRHNYMTGLVARGAAVLRDPTSKWFLSPEVFP
          MVMLEWL.S.C....YAMK.DSD.FLNV.NLV.LLL.APR.NYMTGLVA.GAAVLRDP.SKW.L..E...
Retrocopy MVMLEWLNSYCSSAAYAMKIDSDMFLNVPNLVNLLLKAPRTNYMTGLVAHGAAVLRDPNSKWYLPREILS

Parental  EDSYPPYALGVGYVLSLDLPNQILEASKTIQAVYIEDVYLGLCMRHLGIPLTDPPHGGSFVINTPSETTG
          ED.YPPYALG.GY.LSLDL.....EAS......YIEDVYLGLCMRHLGI..T.PP.....V...P.....
Retrocopy EDVYPPYALGLGYILSLDLTKKLIEASRHVKPLYIEDVYLGLCMRHLGIRPTEPPSYSFHVF--PVRYSR

Parental  CYFASVI-VTLLQNSEQILDVWKAYE
          C.....I..T.LQN.......W....
Retrocopy CEYSKIIATTTLQNMDRVW-IWRDFK

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_15 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_15 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Xiphophorus maculatus	ENSXMAG00000003895	1 retrocopy	retro_xmac_15 ,
Xiphophorus maculatus	ENSXMAG00000018521	1 retrocopy	retro_xmac_19,