RetrogeneDB ID: retro_cpor_1292

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_65:9220191..9221186(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: XIAP
• Ensembl ID: ENSCPOG00000006316
• Aliases: None
• Description: None

Sequence

>retro_cpor_1292
CTATTAAGAACTGGACAGGTTGTAGATATATCAGATACTATATACCCAAGGAATCCTGCCATGTGTAGTGAAGAGCTAGA
TTAAAATCATTTCAGAACTAGCCGGACTATGCCCACTGAACTCCCAGAGAGTTAGCTAGTGCTGGACTCTACTACACAGG
TATTGATGATCAAGTGTAGTGCTTTTGTTGTGGAAAACTGAAAAATTGGGAACCTTGTGATTGTGCCTGGTCAGAACACA
GACGACATTTCCCAAATGCTTCTTTGTTTTGGGTCAGAACATTAATGTTCGAAATGAATCCGATGTGAGTTCTAACAGGA
ATTTCCCAAATTCAACAATTCCTCCAAGAAATTCAGCCATGGCAGAATATGAAGCCTGATCATTACTTTTGGGACATGGA
CGTACTCAGTTAATAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTACAGGTGAAGGCGATAAGGTAAAGTGCTTTC
ACTGTGGAGGAGGATTAACTGATTGGAAGCCCAGTGAAGACCCTTGGGGACAACATGCTAAGTGGTATCCAGGATATAAA
TATCTTTTGGAAGAGAAGAGACAAGAATATATAAACAATATTCATTTAATCCATTCACGTGAGGAGTCTTTGGTAAAAAC
TGCTGAAAAAACACCATCGCTGATGAACAGAATTGATGATACAGTCTTCCACAATCCCATGGTACAAGAAGCTATACGAA
TGGGATTCAGTTTCAGGGATATTAAGAAAATAATGGAGGGAAAAATTCAGACATCTGGGAGCAATTACATATCACTGGAG
GTTCTAGTTGCAGATCTAGTGAGTGTTCAGAAAGATAATACACAAGATGAATCAAGTCAGACTTCATTGCAGAAAGATAT
TAGTACCAAGGAGCAGCTAAGGCGCCTACAAGAAGAGAAGCTTTGCAAAATCTGTATGGATAGAAATATTGCTGTAGTTT
TTATTCCTTGTGGACAGCTGGTCACTTGTAAAGAG

Alignment

ORF - retro_cpor_1292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 67.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLRTGQVVDISDTIYPRNPAMCSEE-ARLKSFHNWPDYAHLTPRELASAGLYYTGIDDQVQCFCCGGKLK
          LLRTGQVVDISDTIYPRNPAMCSEE.ARLKSF.N.PDYAH.TPRELASAGLYYTGIDDQV.CFCCG.KLK
Retrocopy LLRTGQVVDISDTIYPRNPAMCSEE<ARLKSFQN*PDYAH*TPRELASAGLYYTGIDDQV*CFCCG-KLK

Parental  NWEPCDRAWSEHRRHFP-KCFFVLGRNINVRSESDVSSNRNFPNSTIPPRNPAMAEYEARIITFGTWTYS
          NWEPCD.AWSEHRRHFP.KCFFVLG.NINVR.ESDVSSNRNFPNSTIPPRN.AMAEYEA.....G.....
Retrocopy NWEPCDCAWSEHRRHFP<KCFFVLGQNINVRNESDVSSNRNFPNSTIPPRNSAMAEYEA*SLLLGHGRTQ

Parental  VNKEQLARAGFYAL-GEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEEKGQEYINNIHLTHS
          .....L....F....GEGDKVKCFHCGGGLTDWKPSEDPW.QHAKWYPG.KYLLEEK.QEYINNIHL.HS
Retrocopy LIRSSLQELDFMLY>GEGDKVKCFHCGGGLTDWKPSEDPWGQHAKWYPGYKYLLEEKRQEYINNIHLIHS

Parental  LEESLVRTAEKTPSLMKRNDDTVFQNPMVQEAIRMGFSFRDIKKIMEEKIQTSGSNYVSLEVLVADLVSV
          .EESLV.TAEKTPSLM.R.DDTVF.NPMVQEAIRMGFSFRDIKKIME.KIQTSGSNY.SLEVLVADLVSV
Retrocopy REESLVKTAEKTPSLMNRIDDTVFHNPMVQEAIRMGFSFRDIKKIMEGKIQTSGSNYISLEVLVADLVSV

Parental  QKDNTQDESSQTSLQKDISTEEQLRRLQEEKLCKICMDRNIAVVFIPCGHLVTCKE
          QKDNTQDESSQTSLQKDIST.EQLRRLQEEKLCKICMDRNIAVVFIPCG.LVTCKE
Retrocopy QKDNTQDESSQTSLQKDISTKEQLRRLQEEKLCKICMDRNIAVVFIPCGQLVTCKE

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	18.92 RPM
SRP017611_kidney	0.00 RPM	19.26 RPM
SRP017611_liver	0.00 RPM	13.45 RPM
SRP040447_lung	0.00 RPM	11.25 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.44 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1292 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1292 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006316	1 retrocopy	retro_cpor_1292 ,
Oryctolagus cuniculus	ENSOCUG00000009878	1 retrocopy	retro_ocun_82,
Otolemur garnettii	ENSOGAG00000025670	1 retrocopy	retro_ogar_2859,