RetrogeneDB ID: retro_cpor_1461

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_88:615987..616625(-)
• Located in intron of: ENSCPOG00000000142

Retrocopy information

• Ensembl ID: ENSCPOG00000020262
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C18ORF21
• Ensembl ID: ENSCPOG00000025449
• Aliases: None
• Description: None

Sequence

>retro_cpor_1461
ATGAGGCAGAAGTACTATCTTGAGGCTGTGGCGCGAAGCTTACAGGATAGCTGCCCTGGCCAAGCCCGCTATCTCCTCTG
GACCTACTCTTCGTCGCATGATGACAAGAGCACTTTTGAAGAAACGTGTCTGTATTGTTTCCAGTTGTTGGTTCTGGATA
ACTCTCGAGTGCGCCTCAAGCCCAAGGCCAAACTGACACCTAGAATACAGAAACTTCTTAATCCAGAAGCTAGAACTCAT
ACACTTAGTTTTAAAAAAGCAAAAATAGTGAAAAAGTACAGAGACTCCAAAAATGTACTGTTGATTACTTGTAAGACTTG
CAACAGAACAGTTAAACATCATGGTAAAAGTAGAAGCTTTCTGTCAGCATTGAAGAATGTTCCTGCTACTCCTACAAGTA
AACTTGGCCCAAAGAGACCAGAAAAAAAGACTTCAAGCTCCACAAATGTATCTGATTCCAAAGGCCAGAGCCCAGCGTTC
ATTTTCAGAACACCTACATCTGGCCAGTCAACACCCATTTGCTCCTCAAAGAGTGGGAGCAAAAGAAAGAAACACTTCTC
TCAACTAAAAATGTTGCCAGTCAGAGTGAATCCCAAAAGGATCCAAAAGTAGACTTCAAAAGTTTCTTATCTTCACTG

Alignment

ORF - retro_cpor_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRQKHYLEAAARSLQDSCPGQARYLLWTYSSSHDDKSTFEETCPYCFQLLVLDNSRVRLKPKAKLTPRIQ
          MRQK.YLEA.ARSLQDSCPGQARYLLWTYSSSHDDKSTFEETC.YCFQLLVLDNSRVRLKPKAKLTPRIQ
Retrocopy MRQKYYLEAVARSLQDSCPGQARYLLWTYSSSHDDKSTFEETCLYCFQLLVLDNSRVRLKPKAKLTPRIQ

Parental  KLLNREARTHTLSFKEAKIVKKYRDSKNVLSITCKTCNRTVKHHGKSRSFLSALKNVPATPTSKLGPKRP
          KLLN.EARTHTLSFK.AKIVKKYRDSKNVL.ITCKTCNRTVKHHGKSRSFLSALKNVPATPTSKLGPKRP
Retrocopy KLLNPEARTHTLSFKKAKIVKKYRDSKNVLLITCKTCNRTVKHHGKSRSFLSALKNVPATPTSKLGPKRP

Parental  EKKTSSSTDVSDSKGQSPAFIFRTPPSGQSTPICSSKSGSKRKKHFSQLKML-LSQSESQKDPKVDFKSF
          EKKTSSST.VSDSKGQSPAFIFRTP.SGQSTPICSSKSGSKRKKHFSQLKML..SQSESQKDPKVDFKSF
Retrocopy EKKTSSSTNVSDSKGQSPAFIFRTPTSGQSTPICSSKSGSKRKKHFSQLKML<ASQSESQKDPKVDFKSF

Parental  LSSL
          LSSL
Retrocopy LSSL

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	5.87 RPM
SRP017611_kidney	0.00 RPM	8.48 RPM
SRP017611_liver	0.04 RPM	4.14 RPM
SRP040447_lung	0.03 RPM	6.68 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1461 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1461 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029548	1 retrocopy	retro_cfam_1636,
Callithrix jacchus	ENSCJAG00000021041	2 retrocopies	retro_cjac_1030, retro_cjac_2169,
Cavia porcellus	ENSCPOG00000025449	1 retrocopy	retro_cpor_1461 ,
Felis catus	ENSFCAG00000000626	1 retrocopy	retro_fcat_1717,
Homo sapiens	ENSG00000141428	1 retrocopy	retro_hsap_3062,
Gorilla gorilla	ENSGGOG00000026334	1 retrocopy	retro_ggor_2102,
Macaca mulatta	ENSMMUG00000018782	1 retrocopy	retro_mmul_1876,
Monodelphis domestica	ENSMODG00000025605	1 retrocopy	retro_mdom_260,
Mus musculus	ENSMUSG00000024273	2 retrocopies	retro_mmus_1676, retro_mmus_610,
Nomascus leucogenys	ENSNLEG00000006237	1 retrocopy	retro_nleu_1655,
Oryctolagus cuniculus	ENSOCUG00000028046	2 retrocopies	retro_ocun_1910, retro_ocun_435,
Ochotona princeps	ENSOPRG00000011163	2 retrocopies	retro_opri_1222, retro_opri_283,
Pongo abelii	ENSPPYG00000009110	1 retrocopy	retro_pabe_2536,
Pan troglodytes	ENSPTRG00000009973	2 retrocopies	retro_ptro_1981, retro_ptro_2935,
Pteropus vampyrus	ENSPVAG00000009174	3 retrocopies	retro_pvam_1086, retro_pvam_1488, retro_pvam_629,
Tupaia belangeri	ENSTBEG00000016670	1 retrocopy	retro_tbel_4056,
Tarsius syrichta	ENSTSYG00000010817	2 retrocopies	retro_tsyr_1675, retro_tsyr_1787,