RetrogeneDB ID: retro_cpor_848

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:9188667..9189447(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000023465
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000009226
• Aliases: None
• Description: None

Sequence

>retro_cpor_848
TATGGCACAAACGATCCTGTTCCAGGCTATTCTTTTCCAGCAGCAGAACGTAGTACAATTACAACTTGGGAGAAAGACCA
TAAAAAGGATGCTTGTGAACATATATTTAACACAGTTTTCATCAGTGCCTGTATCCGTGGTCAGCAATAGCTATGACATT
TATAATGCATGTGAGAAAACTTGGGGTGAAAATCTATGACATTTAATACTGTCGAGAAGCACAGAGGCACCATTAATGAT
CAGACCTGATTGTGGAAATCCTTTTGAAACTGTATTAAAGGTTTTTGATATTTTAGGTAAGAAATTTCCTGTTACTGTGA
ACTCAAAAGGCTATGCATTGCTGCCACCTTATCTTAGAGTTATTCAAGGGGATGGATTAGATATTAATACCTTATAAGAG
ATTGTAGAAGGCATGAAGCAAAAAAAGTGGAGCATTGAAGATGTTTCCTTTAATTCTGGTGGAGCTTTGCTACAGAAGGT
AACCAGAGATCTCCTGAATTGTTCCTCCAAGTGTAGCTATGTTGTCACCAATGGTCTTGGGATTAATGTCTTTAAAGACC
CAGTAGCTGATTCCAACAAAAGGTCCCAAAAGGGCCCCTTATCATTACACAGGACACCAGCAGGGTCCTTACGCTTGAGG
AAGGAAAAGGAGACCTTGAAGAATATGGTCAGGATCTTCTCCACACTGTCTTCAAGAATGGGAAGGTGACTAAAAGCCAT
TCATTTGATGAAATAAGAAAGAATGCACGACTGAACAGAGACCTGGAAGCAGCCCCTCAT

Alignment

ORF - retro_cpor_848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 55.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHI-VTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLI
          YGT.DPVPGYS.PAAE.STIT.W.KDH.KDA.EHI..TQFSSVPVSVVS.SYDIYNACEK.WGE.L.HLI
Retrocopy YGTNDPVPGYSFPAAERSTITTWEKDHKKDACEHI>LTQFSSVPVSVVSNSYDIYNACEKTWGENL*HLI

Parental  LSRSTEAPLIIRPDSGNPLDTVLKVLDILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMK
          LSRSTEAPL.IRPD.GNP..TVLKV.DILGKKFPVT.NSKGY.LLPPYLRVIQGDG.DINTL.EIVEGMK
Retrocopy LSRSTEAPLMIRPDCGNPFETVLKVFDILGKKFPVTVNSKGYALLPPYLRVIQGDGLDINTL*EIVEGMK

Parental  QKRWSIENVSFGSGGALLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGN
          QK.WSIE.VSF.SGGALLQK.TRDLLNCS.KCSYVVTNGLGINVFKDPVAD.NKRS.KG.LSLHRTPAG.
Retrocopy QKKWSIEDVSFNSGGALLQKVTRDLLNCSSKCSYVVTNGLGINVFKDPVADSNKRSQKGPLSLHRTPAGS

Parental  FVTLEEGK-GDLEEYGQDLLHTVFKNGKVTRSYSFDEVRKNARLNIELEAAPH
          ...L...K.GDLEEYGQDLLHTVFKNGKVT.S.SFDE.RKNARLN..LEAAPH
Retrocopy -LRLRKEK<GDLEEYGQDLLHTVFKNGKVTKSHSFDEIRKNARLNRDLEAAPH

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	19.96 RPM
SRP017611_kidney	0.00 RPM	75.17 RPM
SRP017611_liver	0.00 RPM	41.31 RPM
SRP040447_lung	0.00 RPM	37.25 RPM
SRP040447_skeletal_muscle	0.00 RPM	43.57 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_848 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_848 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016193	2 retrocopies	retro_cjac_1281, retro_cjac_3877,
Cavia porcellus	ENSCPOG00000009226	1 retrocopy	retro_cpor_848 ,
Homo sapiens	ENSG00000105835	1 retrocopy	retro_hsap_79,
Oryctolagus cuniculus	ENSOCUG00000013417	1 retrocopy	retro_ocun_777,
Pongo abelii	ENSPPYG00000018270	2 retrocopies	retro_pabe_1407, retro_pabe_1415,
Pan troglodytes	ENSPTRG00000019571	1 retrocopy	retro_ptro_114,
Takifugu rubripes	ENSTRUG00000016695	1 retrocopy	retro_trub_33,