RetrogeneDB ID: retro_cpor_1460

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_88:449696..450536(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000010887
• Aliases: None
• Description: None

Sequence

>retro_cpor_1460
CAAGAAGGATCACTTTGTGCTCAACATTGCCTGAATAATCTATTGCAAGGAGAATATTTTAGCCCTGTGGAGTTATCCTC
AATTGCCCACCAGCTGGATGAAGAAGAAAGGATGAGAATGGCAGAAGGAGGGGTTACTAGTGAAGACTATCGCACGTTTT
TACAGCAGCCTTCTGGAAATATGGATGACAGTGGCTTTTTCTCTATTCAAGTTATAAGCAATGCCTTGAAAATTTGGGGT
TTGGAACTAATCCTGTTCAACAGTCCAGAGTATCAGCGGCTCAGGATTGATCCTATAAATGAAAAGTCATTTATATGCAA
TTATAAAGAACACTGGTTTATAGTTAGAAAATTAGGAAAACAGTGGTTTAACTTGAATTCTTTCTTGACGGGTCCAGAAT
TAATATCAGATACATACCTTGCACTTTTCTTGGCTCAATTACAACAGGAAGGTTATTCTATATTTGTTGTTAAGGGTGAT
CTGCCAGATTGTGAAGCTGACCAACTTTTCCAGATGATCAGGGTCCAACAGATGCATTGACCAAAACTCATTGGAGAAGA
GTTAGCACAACTGAAAGAGCAGAGAGTCCTTAAAACAGACCTGGAACAAGTCTTAGAAGGAAATAATAGGCTGGGAATGT
TAGATGAAGAGGATTTGCAGAGGGCACTGGCATTAAGTCGGCAGCAGATTGACATGGAAGATGAAGAAGCAGATCTTCGC
AGGGCTATTCAGCTCAGTATGCAAGGGGGTTCCAGAAATATATCTCAAGATGTTGCACAGACATCAGGCACAAATCTTAC
ATTTGAAGAGCTGCGAAGGAGAAGAGAAGCCTTCTTTGAA

Alignment

ORF - retro_cpor_1460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.41 %
• Parental protein coverage: 77.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMDDSGFFSIQ
          QEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMDDSGFFSIQ
Retrocopy QEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMDDSGFFSIQ

Parental  VISNALKVWGLELILFNSPEYQRLRIDPINEKSFICNYKEHWFTVRKLGKQQWFNLNSLLTGPELISDTY
          VISNALK.WGLELILFNSPEYQRLRIDPINEKSFICNYKEHWF.VRKLGK.QWFNLNS.LTGPELISDTY
Retrocopy VISNALKIWGLELILFNSPEYQRLRIDPINEKSFICNYKEHWFIVRKLGK-QWFNLNSFLTGPELISDTY

Parental  LALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVLKTDLEQVLEGND
          LALFLAQLQQEGYSIFVVKGDLPDCEADQL.QMIRVQQMH.PKLIGEELAQLKEQRVLKTDLEQVLEGN.
Retrocopy LALFLAQLQQEGYSIFVVKGDLPDCEADQLFQMIRVQQMH*PKLIGEELAQLKEQRVLKTDLEQVLEGNN

Parental  GSGMLDEDEEDLQRALALSRQQIDMEDEEADLRRAIQLSMQGGSRNISQDVAQTSGTDLTFEELRRRREA
          ..GML..DEEDLQRALALSRQQIDMEDEEADLRRAIQLSMQGGSRNISQDVAQTSGT.LTFEELRRRREA
Retrocopy RLGML--DEEDLQRALALSRQQIDMEDEEADLRRAIQLSMQGGSRNISQDVAQTSGTNLTFEELRRRREA

Parental  YFE
          .FE
Retrocopy FFE

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	9.49 RPM
SRP017611_kidney	0.63 RPM	9.42 RPM
SRP017611_liver	0.39 RPM	10.88 RPM
SRP040447_lung	0.08 RPM	9.46 RPM
SRP040447_skeletal_muscle	0.03 RPM	2.10 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1460 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1460 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005786	2 retrocopies	retro_btau_1652, retro_btau_330,
Choloepus hoffmanni	ENSCHOG00000005302	1 retrocopy	retro_chof_2238,
Callithrix jacchus	ENSCJAG00000018025	2 retrocopies	retro_cjac_1724, retro_cjac_375,
Cavia porcellus	ENSCPOG00000010887	1 retrocopy	retro_cpor_1460 ,
Homo sapiens	ENSG00000066427	1 retrocopy	retro_hsap_89,
Macaca mulatta	ENSMMUG00000020751	1 retrocopy	retro_mmul_298,
Monodelphis domestica	ENSMODG00000002006	2 retrocopies	retro_mdom_1498, retro_mdom_1573,
Nomascus leucogenys	ENSNLEG00000017126	1 retrocopy	retro_nleu_66,
Pongo abelii	ENSPPYG00000006075	1 retrocopy	retro_pabe_9,
Pteropus vampyrus	ENSPVAG00000015316	2 retrocopies	retro_pvam_1201, retro_pvam_587,
Tupaia belangeri	ENSTBEG00000008099	3 retrocopies	retro_tbel_102, retro_tbel_2635, retro_tbel_3925,