RetrogeneDB ID: retro_xmac_8

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH557118.1:165198..165510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019612
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: inip (1 of 2)
• Ensembl ID: ENSXMAG00000002259
• Aliases: None
• Description: ints3 and nabp interacting protein [Source:ZFIN;Acc:ZDB-GENE-040426-961]

Sequence

>retro_xmac_8
ATGGCCGCCAACCCTCCCGGACAGGGCTTCCAGAACAAAACCCGAGTGGCCATCCTGGCGGAACTGGACAAGGAGAAGCG
GCGGCTGATGCAGGGCCAGTCCATGAACAGCCCCGGAGCCAACATCCCGCTCTCGGGCCGGGGCAGCCTGAAGGAGGCGA
GGGACAGCGCGGAGCAGCAGCACATCGCCGCCCAGCAGAAGGCCGCCCTGCAGCACGCTCACGTCCACTCCTCCGGCTTC
TTCATCACCCAGGACTCCTCGTTCGGGAACCTCATCCTCCCGGTGCTTCCCCGCCTGGAGCCCGACCTCTGA

Alignment

ORF - retro_xmac_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.19 %
• Parental protein coverage: 98.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANPPGQAIPSKARVAILAELEKEKRRLRENQSMNVPGASIPLS-RPNMKEFRDSAELQHIAAQQRAAL
          MAANPPGQ....K.RVAILAEL.KEKRRL...QSMN.PGA.IPLS.R...KE.RDSAE.QHIAAQQ.AAL
Retrocopy MAANPPGQGFQNKTRVAILAELDKEKRRLMQGQSMNSPGANIPLSGRGSLKEARDSAEQQHIAAQQKAAL

Parental  QHAHAHSSGFFITQDSSFGNLILPVLPRLEP
          QHAH.HSSGFFITQDSSFGNLILPVLPRLEP
Retrocopy QHAHVHSSGFFITQDSSFGNLILPVLPRLEP

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_8 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_8 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006841	1 retrocopy	retro_amel_1661,
Equus caballus	ENSECAG00000008524	1 retrocopy	retro_ecab_187,
Homo sapiens	ENSG00000148153	1 retrocopy	retro_hsap_2980,
Microcebus murinus	ENSMICG00000001130	1 retrocopy	retro_mmur_92,
Nomascus leucogenys	ENSNLEG00000016554	1 retrocopy	retro_nleu_1508,
Oryctolagus cuniculus	ENSOCUG00000016717	1 retrocopy	retro_ocun_335,
Oryzias latipes	ENSORLG00000011577	1 retrocopy	retro_olat_8,
Pan troglodytes	ENSPTRG00000023472	1 retrocopy	retro_ptro_2015,
Sorex araneus	ENSSARG00000003661	1 retrocopy	retro_sara_104,
Xiphophorus maculatus	ENSXMAG00000002259	1 retrocopy	retro_xmac_8 ,