RetrogeneDB ID: retro_cpor_110

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:136238..136865(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025412
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000003374
• Aliases: None
• Description: None

Sequence

>retro_cpor_110
GAAGCACAGAATGGATCAGAATTGGAGGCTAGGACTCAGTCAAAAATCAAGTATGACTGGTATCAAACAGAATCTCAAGT
AATTATGACACTTATGATTAAGAATGTTCAGAAGAATGATGTAAATGTGGAATTTTCAGAAAAAGAGTTATTTGCTTTGG
TGAAACTTTCTTCTGGAGAAGATTACAATTTGAAACCGAGACTGCTTCATCCTATAATACCAGAACAGAGCACATTTAGA
GAACTTTCAAAAAAGATTGAAATTAAAATGAAAAAGCCAGAGGCTGTGAGATGGGAAAAACTAGAGGGGCAAGGAGATGT
GCCTACGTCCAAACAGTTCATAGCAGATGTAAAGAACTTATATCCGTCATCATCTCATTATACAAGAAATTGGGATAAGT
TGGTTGGTGAGATCAAAGAAGAAGAAAAGAATGAGAAATCAGAGGGAGATGCAGCTTTAAACAAGTTATTTCAGCAGATC
TATTCAGATGGCTTTGATGAAGTCAAACGTGCCATGAACAAATCATTTATGGAATCTGGTGGTACAGTTTTGAGTACCAA
CTGGTCTGATGTCAGTAAAAGGAAAGTTGAAATCAATCCTGCTGATGATATGGAATGGGAAAAATAC

Alignment

ORF - retro_cpor_110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 57.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAQNGKNQKVIYNQKKNRYDWYQTESQVIITLMIKNVQKNDVNVEFSEKELFALVKLSSGEDYNLKLRLL
          EAQNG........Q.K..YDWYQTESQVI.TLMIKNVQKNDVNVEFSEKELFALVKLSSGEDYNLK.RLL
Retrocopy EAQNGSELEA-RTQSKIKYDWYQTESQVIMTLMIKNVQKNDVNVEFSEKELFALVKLSSGEDYNLKPRLL

Parental  HPIIPEQSTFRVLSTKIEIKMKKPEAVRWEKLEGQGDVPASKQFIADVKNLYPSSSHYTRNWDKLVGEIK
          HPIIPEQSTFR.LS.KIEIKMKKPEAVRWEKLEGQGDVP.SKQFIADVKNLYPSSSHYTRNWDKLVGEIK
Retrocopy HPIIPEQSTFRELSKKIEIKMKKPEAVRWEKLEGQGDVPTSKQFIADVKNLYPSSSHYTRNWDKLVGEIK

Parental  EEEKNEKLEGDAALNKLFQQIYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMEWKKY
          EEEKNEK.EGDAALNKLFQQIYSDG.DEVKRAMNKSFMESGGTVLSTNWSDV.KRKVEINP.DDMEW.KY
Retrocopy EEEKNEKSEGDAALNKLFQQIYSDGFDEVKRAMNKSFMESGGTVLSTNWSDVSKRKVEINPADDMEWEKY

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	1.09 RPM	17.25 RPM
SRP017611_kidney	1.99 RPM	26.49 RPM
SRP017611_liver	2.35 RPM	22.63 RPM
SRP040447_lung	1.26 RPM	21.77 RPM
SRP040447_skeletal_muscle	1.21 RPM	17.58 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_110 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_110 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353, retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110 ,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773,