RetrogeneDB ID: retro_cpor_1416

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:33265405..33265756(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEB2
• Ensembl ID: ENSCPOG00000021024
• Aliases: None
• Description: None

Sequence

>retro_cpor_1416
CAGGACTTGTTCCTCATGATCTGGCGCCACAAGACCACCATCTTCACGACACCAAGGAGCACCATGTTCGAGCTGAAGTG
CATCCTCGAGGGCGTCCTCAAGCGGCCACCCCAGGAGCAGAGGCTTTGCAAGGATGACTAGCTACTAGATAACGGTAAAA
CGCTGGGCGAGTGTGGTTTTACCAGCCAGACATCAAGGAGGCCACAAGCCCCAGCCACAGTGGGCCTGGCCTTCCGGGCA
GATGATACCTTTGAGGCCCTGCGCATTGAGGCCTTCTCTAGCCCACCGGAGCTTCCAGAAGTCATGAAGCCTCAGGACTC
TGGAGGTAGCGCCAGTGAACAAGCTGTGCAG

Alignment

ORF - retro_cpor_1416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTA-RP
          QD.FLMI.RHKTTIFT.....ST.FELK.I.EG.LKRPP.EQRL.KDD.LLD.GKTLGECGFTSQT..RP
Retrocopy QDLFLMIWRHKTTIFTTPR--STMFELKCILEGVLKRPPQEQRLCKDD*LLDNGKTLGECGFTSQTSRRP

Parental  QAPATVGLAFRADDTFEALRIEPFSSPPELPDVMKPQDSGGSANEQAVQ
          QAPATVGLAFRADDTFEALRIE.FSSPPELP.VMKPQDSGGSA.EQAVQ
Retrocopy QAPATVGLAFRADDTFEALRIEAFSSPPELPEVMKPQDSGGSASEQAVQ

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	24.16 RPM
SRP017611_kidney	0.00 RPM	66.58 RPM
SRP017611_liver	0.00 RPM	48.58 RPM
SRP040447_lung	0.00 RPM	52.36 RPM
SRP040447_skeletal_muscle	0.01 RPM	74.55 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1416 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1416 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 15 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019543	3 retrocopies	retro_btau_142, retro_btau_17, retro_btau_29,
Callithrix jacchus	ENSCJAG00000015347	10 retrocopies	retro_cjac_1593, retro_cjac_1606, retro_cjac_2051, retro_cjac_2613, retro_cjac_2987, retro_cjac_3030, retro_cjac_342, retro_cjac_3819, retro_cjac_639, retro_cjac_959,
Cavia porcellus	ENSCPOG00000021024	1 retrocopy	retro_cpor_1416 ,
Felis catus	ENSFCAG00000004711	2 retrocopies	retro_fcat_112, retro_fcat_40,
Homo sapiens	ENSG00000103363	2 retrocopies	retro_hsap_1246, retro_hsap_940,
Gorilla gorilla	ENSGGOG00000015306	1 retrocopy	retro_ggor_976,
Monodelphis domestica	ENSMODG00000016536	4 retrocopies	retro_mdom_1149, retro_mdom_1617, retro_mdom_1964, retro_mdom_23,
Mustela putorius furo	ENSMPUG00000015265	1 retrocopy	retro_mputfur_469,
Mus musculus	ENSMUSG00000055839	7 retrocopies	retro_mmus_1212, retro_mmus_1489, retro_mmus_1664, retro_mmus_2930, retro_mmus_511, retro_mmus_747, retro_mmus_99,
Nomascus leucogenys	ENSNLEG00000009471	2 retrocopies	retro_nleu_295, retro_nleu_89,
Oryctolagus cuniculus	ENSOCUG00000010116	2 retrocopies	retro_ocun_202, retro_ocun_930,
Pongo abelii	ENSPPYG00000007013	1 retrocopy	retro_pabe_74,
Pan troglodytes	ENSPTRG00000007663	1 retrocopy	retro_ptro_857,
Rattus norvegicus	ENSRNOG00000004814	6 retrocopies	retro_rnor_1226, retro_rnor_1275, retro_rnor_185, retro_rnor_1948, retro_rnor_35, retro_rnor_352,
Sus scrofa	ENSSSCG00000008061	1 retrocopy	retro_sscr_858,