RetrogeneDB ID: retro_cpor_1340

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:48927457..48927985(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX11
• Ensembl ID: ENSCPOG00000008482
• Aliases: None
• Description: None

Sequence

>retro_cpor_1340
TGTGGCTGGCCTGGGAGCCGCCGTGGCTCCTTGAACAGGACTGCAGAGCAGATAGAGCCATTGCTTCAGCTGGAATGGAA
GGAAATGAGAGTTGATACAAGGGCCTGAAGCAGCTCAGGACAAAGAAGCGCTGGAGACTTGTCCGGGATCCGAGCTTGGA
GCCGCCATTGGCAGCCGAGACGCTGGGACCCTTTCGCGCATGCGCAGAAGGAGGACTGGCGTTGGTGGAACAGGACTGGC
CTCACCCACTTACGTGGCCTGGTCGCTGTGGGCAAGTAGAGGGTGTCCTGCTCTGCCAGGGCCTCGTATCGGCTGTTGCC
CACTACTGGTCTTGGAGGGTCAGTAGTTACAGGTCACGCATCAAACCAGATTGAAAACAAGGTGCATGTTGAAGATCCAC
TCATGAAGGTGACCCTGAGTACAAATGTGCACGCCTCCCTCCAGTGGAATTGTAGGCCTCAGAATGCAGAAATATATGTG
GTATCTGGAGAGACTGCGGTGCCATTTTACAAAGCTAAGGATCCTACT

Alignment

ORF - retro_cpor_1340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.07 %
• Parental protein coverage: 64.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CGWSWGHLGSLTRTAEQIEPFLLPGWRGTGVADR-GLRRLGTWKRPSPARGPTAE-QQWRPKSTNPFTRA
          CGW.....GSL.RTAEQIEP.L...W....V..R.GL..L.T.KR....R.P..E...W.P....PF..A
Retrocopy CGWPGSRRGSLNRTAEQIEPLLQLEWKEMRVDTR<GLKQLRTKKRWRLVRDPSLE>RHWQPRRWDPFAHA

Parental  QEEDWRRRNKTVLTYV-AAAAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHGSDQIESMVPVKDRIIKV
          Q.EDWR..N.T.LT......AVG....S..A...YRL...TTGLGGS.V.GH.S.QIE..V.V.D...KV
Retrocopy QKEDWRWWNRTGLTHLRGLVAVGK*RVSCSARASYRL-LPTTGLGGSVVTGHASNQIENKVHVEDPLMKV

Parental  TFNADVHASLQWNFRPQQSEIYVVPGETALAFYKARNPT
          T....VHASLQWN.RPQ..EIYVV.GETA..FYKA..PT
Retrocopy TLSTNVHASLQWNCRPQNAEIYVVSGETAVPFYKAKDPT

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	8.17 RPM
SRP017611_kidney	0.00 RPM	21.15 RPM
SRP017611_liver	0.00 RPM	13.62 RPM
SRP040447_lung	0.00 RPM	5.93 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1340 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1340 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340 ,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,