RetrogeneDB ID: retro_cpor_1008

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:21260687..21261127(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11ORF57
• Ensembl ID: ENSCPOG00000011060
• Aliases: None
• Description: None

Sequence

>retro_cpor_1008
ATATCCTAGGTTCAGCTGGGGAAGATTCTCCTTAGCAATGCTATCCAGCACACATATGCTCACAATAAGATCCAGGAACA
AACAGATACGTGAAAAATAAGAGAATACAGAAACAGATGAAGGATACTTACCAGGAAACCAAAAGGAAAATGTTACCCAG
CTGTTCAAGTCAGATGCATAGTAATGATTTTGAGGAAGAAAGTCAGAGAGAATATTGGAGGCCAAAAACAGTTTTCCTGA
ACACTGGAAGAGGATTTTCTTAAGGCTAAATTCTGGCACAAAAAGACACATGGTTATGAACCTATCATACTAGGCCAATA
AGTTCACAGTGGTTATGAGTTTGAAGACTTTGAAACGGACAGTAGTGATCAGTCAGATATTACCAATGGGGAAAAAAATC
CCCCCAGATAAAATCATCCCACAAACATAAGAAGTTCCAC

Alignment

ORF - retro_cpor_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 51.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSRVPLGKVLLRNVIRHTDAHNKIQEESDMWKIRE-IEKQMEDTYQETKRKMLPSSSSRMRSDGFDEESQ
          .S.V.LGK.LL.N.I.HT.AHNKIQE..D..KIRE.I.KQM.DTYQETKRKMLPS.SS.M.S..F.EESQ
Retrocopy IS*VQLGKILLSNAIQHTYAHNKIQEQTDT*KIRE<IQKQMKDTYQETKRKMLPSCSSQMHSNDFEEESQ

Parental  REYWRPKTEITGT-LEEDFLKAKS-WNKKLYDYEANMPDRWGHSGYKELYPEEFETDSSDQQDITNGKKT
          REYWRPKT....T.....FL...S.W.KK...YE........HSGY.....E.FETDSSDQ.DITNG.K.
Retrocopy REYWRPKTVFLNT<WKRIFLRLNS<WHKKTHGYEPIILGQ*VHSGYEF---EDFETDSSDQSDITNGEKN

Parental  -SPQIKSSTHESRKH
          .SPQIKSS......H
Retrocopy <SPQIKSSHKHKKFH

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	14.26 RPM
SRP017611_kidney	0.00 RPM	23.03 RPM
SRP017611_liver	0.00 RPM	11.75 RPM
SRP040447_lung	0.00 RPM	14.91 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.47 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1008 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1008 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001999	1 retrocopy	retro_btau_1726,
Cavia porcellus	ENSCPOG00000011060	1 retrocopy	retro_cpor_1008 ,
Monodelphis domestica	ENSMODG00000014393	1 retrocopy	retro_mdom_351,
Tursiops truncatus	ENSTTRG00000010518	1 retrocopy	retro_ttru_73,