RetrogeneDB ID: retro_cpor_105

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_37:3022741..3023644(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000003893
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000005570
• Aliases: None
• Description: None

Sequence

>retro_cpor_105
ATGAAATCCAGTCCTGCCATCCAAGCTGCCATTGACCTCACAGCGGGGGCTGCAGGGGGCACCGCATGTGTACTGACCGG
GCAGCCCTTCGACACCATGAAGGTGAAGATGCAGACGTTCCCTGACCTGTACCGGGGCCTCACCGACTGCTGCCTGAAGA
CCTACTCACAGGTGGGCTTCCGTGGCTTCTACAAGGGCACCAGCCCAGCGCTGATTGCCAACATCGCCGAGAACTCGGTG
CTCTTCATGTGCTATGGCTTTTGCCAGCAGCTGGTGCGGAGAGTGGTTGGACTGGACAGGAAAGCAAAGCTCAGTGACCT
GCAGAATGCCGCCGCGGGATCCGTGGCCTCCGCCTTCGCGGCACTGGTGCTGTGCCCCACGGAGCTTGTGAAGTGCCGGC
TGCAGACCATGTTCGAAATGGAGACGTCAGGAAAGATAACCAGAAGCCAGAATACAGTTTGGTCTGTCGTGAAGAGTATC
CTTAGGAAGGATGGTCCCCTGGGCTTCTACCACGGACTCTCAAGCACCTTACTGCGGGAAGTACCAGGCTATTTCTTCTT
TGGAGGCTATGAACTGAGCCGATCATTTTTGGCATCAGGGAGATCAAAAGATGAGCTAGGTCCTGTCCCTTTGATGTTAA
GCGGTGGAGTTGGTGGAATTTGCCTGTGGCTTGCTGTATACCCAGTGGATTGTGTCAAATCCAGAATTCAAATCCTTTCC
ATGTCTGGGAAACAGGCAGGATTTATTGGAACCCTTCTAAGTGTTGTGAGAAATGAAGGAATAGCAACTTTGTATTCCGG
ACTGAAACCAACCATGATTCGAGCCTTCCCTGCCAATGGCGCACTATTTTTGGTCTACGAATACAGCAGGAAGTTGATGA
TGGGCCAGCTGGAAGCCTTCTGA

Alignment

ORF - retro_cpor_105 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSSPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
          MKSSPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
Retrocopy MKSSPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA

Parental  LIANIAENSVLFMCYGFCQQLVRRVVGLDRKAKLSDLQNAAAGSVASAFAALVLCPTELVKCRLQTMFEM
          LIANIAENSVLFMCYGFCQQLVRRVVGLDRKAKLSDLQNAAAGSVASAFAALVLCPTELVKCRLQTMFEM
Retrocopy LIANIAENSVLFMCYGFCQQLVRRVVGLDRKAKLSDLQNAAAGSVASAFAALVLCPTELVKCRLQTMFEM

Parental  ETSGKITRSQNTVWSVVKSILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFLASGRSKDELGPV
          ETSGKITRSQNTVWSVVKSILRKDGPLGFYHGLSSTLLREVPGYFFF.GGYELSRSFLASGRSKDELGPV
Retrocopy ETSGKITRSQNTVWSVVKSILRKDGPLGFYHGLSSTLLREVPGYFFF-GGYELSRSFLASGRSKDELGPV

Parental  PLMLSGGVGGICLWLAVYPVDCVKSRIQILSMSGKQAGFIGTLLSVVRNEGIATLYSGLKPTMIRAFPAN
          PLMLSGGVGGICLWLAVYPVDCVKSRIQILSMSGKQAGFIGTLLSVVRNEGIATLYSGLKPTMIRAFPAN
Retrocopy PLMLSGGVGGICLWLAVYPVDCVKSRIQILSMSGKQAGFIGTLLSVVRNEGIATLYSGLKPTMIRAFPAN

Parental  GALFLAYEYSRKLMMGQLEAF
          GALFL.YEYSRKLMMGQLEAF
Retrocopy GALFLVYEYSRKLMMGQLEAF

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	0.17 RPM	5.00 RPM
SRP017611_kidney	0.73 RPM	11.83 RPM
SRP017611_liver	1.04 RPM	44.92 RPM
SRP040447_lung	0.25 RPM	5.35 RPM
SRP040447_skeletal_muscle	0.30 RPM	5.48 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_105 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_105 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017797	1 retrocopy	retro_cjac_1776,
Cavia porcellus	ENSCPOG00000005570	2 retrocopies	retro_cpor_105 , retro_cpor_107,
Equus caballus	ENSECAG00000007666	1 retrocopy	retro_ecab_72,
Homo sapiens	ENSG00000102743	1 retrocopy	retro_hsap_44,
Gorilla gorilla	ENSGGOG00000025261	1 retrocopy	retro_ggor_2294,
Microcebus murinus	ENSMICG00000007218	1 retrocopy	retro_mmur_18,
Macaca mulatta	ENSMMUG00000022585	1 retrocopy	retro_mmul_199,
Nomascus leucogenys	ENSNLEG00000001185	1 retrocopy	retro_nleu_1704,
Otolemur garnettii	ENSOGAG00000009380	1 retrocopy	retro_ogar_490,
Pongo abelii	ENSPPYG00000005307	1 retrocopy	retro_pabe_82,
Pan troglodytes	ENSPTRG00000005809	1 retrocopy	retro_ptro_2303,
Pteropus vampyrus	ENSPVAG00000010393	1 retrocopy	retro_pvam_15,
Ictidomys tridecemlineatus	ENSSTOG00000007840	1 retrocopy	retro_itri_726,
Tupaia belangeri	ENSTBEG00000017239	1 retrocopy	retro_tbel_4583,