RetrogeneDB ID: retro_cpor_1143

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:58258024..58258538(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000015439
• Aliases: None
• Description: None

Sequence

>retro_cpor_1143
AATGTCAAGTTCCCAGATGAGGATGCAATACTAGAAAAAGACGAAGCTTTAGAAGATGAAGACAACAAAAATGATGATGG
TATTTCATTCATTAACGAGACAGGCCCTGCTTGGGCAGGCTCAGAGGGAGACTATATGTAATGAGGAGCTATTGAATAGA
GTATTCAACATCATGAGGGAAAAGAATCCAGATATGATCGCAGGAGAGAAAAGAAAATTTGTCATGAAACCTCCACAGGT
CGTCCAAGTGGGAATCAAGAAAATTTCTTTTATTAACTTTACAGATATCTGTAAACTATTACATCATCAGCCCAAACATC
TTCTTGCATTTTTATTGGTAGAATTAGGTACAAGTGGTTCTATAAATGGTAATAACTGACTAGTAATCAAAGGCAGATTT
CAACAGAAACAGATAGAAAATGTCTTAAGAACATATATCAAAGAGTATGTCACTTGTCACACATGCCGGTCTCCAGACAC
AATTCTGCAGAAGGACACCCGGCTCTCTTTCTTA

Alignment

ORF - retro_cpor_1143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.95 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVKFPDEDEILEKDEALEDEDNKKDDGISFSNQTGPAWAGSERDYT-YEELLNRVFNIMREKNPDMVAGE
          NVKFPDED.ILEKDEALEDEDNK.DDGISF.N.TGPAWAGSE.DY...EELLNRVFNIMREKNPDM.AGE
Retrocopy NVKFPDEDAILEKDEALEDEDNKNDDGISFINETGPAWAGSEGDYM>NEELLNRVFNIMREKNPDMIAGE

Parental  KRKFVMKPPQVVRVGTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIE
          KRKFVMKPPQVV.VG.KK.SF.NFTDICKLLH.QPKHLLAFLL.ELGTSGSI.GNN.LVIKGRFQQKQIE
Retrocopy KRKFVMKPPQVVQVGIKKISFINFTDICKLLHHQPKHLLAFLLVELGTSGSINGNN*LVIKGRFQQKQIE

Parental  NVLRRYIKEYVTCHTCRSPDTILQKDTRLYFL
          NVLR.YIKEYVTCHTCRSPDTILQKDTRL.FL
Retrocopy NVLRTYIKEYVTCHTCRSPDTILQKDTRLSFL

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	32.27 RPM
SRP017611_kidney	0.00 RPM	53.18 RPM
SRP017611_liver	0.00 RPM	49.05 RPM
SRP040447_lung	0.00 RPM	47.31 RPM
SRP040447_skeletal_muscle	0.01 RPM	86.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1143 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1143 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143 ,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Homo sapiens	ENSG00000125977	3 retrocopies	retro_hsap_2176, retro_hsap_2260, retro_hsap_713,
Gorilla gorilla	ENSGGOG00000015546	5 retrocopies	retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus	ENSMICG00000006944	1 retrocopy	retro_mmur_1583,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Macaca mulatta	ENSMMUG00000018095	1 retrocopy	retro_mmul_1483,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
Nomascus leucogenys	ENSNLEG00000010034	2 retrocopies	retro_nleu_2242, retro_nleu_466,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Pan troglodytes	ENSPTRG00000013412	2 retrocopies	retro_ptro_1600, retro_ptro_508,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,