RetrogeneDB ID: retro_cpor_258

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:22708711..22709152(-)
• Located in intron of: ENSCPOG00000010889

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000020956
• Aliases: None
• Description: None

Sequence

>retro_cpor_258
ATGGCTATCCCCTCTACAGAGCAGCTGGGCTCCTTCAGATCCAGCGACCTATAGAGCTTGGCCAACAGGCTGGGCCTCCA
GACTAACCTGAGGCAGACAAGCTGTTAAAGGCTTTGAAAACCCACCTTAAACAAGAAACAGAAAAAAGAAAGTAAGAATC
AGGATGAAAGTCAAACTTTTCAGTCCTCCTGTGAGGAGAGTGTGGAACAGATGAACATCAGAGAACAAGCTGAGGAGCCA
GTGGGCCACATCACCACAATAAGGAGGCACCACCAGACGGTCCACAGAGACCCCACTTCCCAGCATCATTCTGAGATATG
CCTGAGTCATCGTACTGAACCACAGAATCAAGAAGACCAGGAACACTGGGATCTCAGAACTACTGGAAAAATTCCTTCTC
TATCAGACAAGCGTCTTGTGGATAAGCATGCAGTTTCCTCA

Alignment

ORF - retro_cpor_258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.56 %
• Parental protein coverage: 86.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTVPSAEELDSFKYSDLQNLAKRLGLRANLR-ADKLLKALKTHLKQ-KANKENKNQDESQAFQSSCDENE
          M..PS.E.L.SF..SDL..LA.RLGL..NLR.ADKLLKALKTHLKQ.K..KE.KNQDESQ.FQSSC.E..
Retrocopy MAIPSTEQLGSFRSSDL*SLANRLGLQTNLR<ADKLLKALKTHLKQ>KQKKESKNQDESQTFQSSCEESV

Parental  VQINGKEQTEKEAEEHITKTRRRRQTVYWNPASRQEHSEISLNHLTESQNQEDQENRELGTTGKIPFLSD
          .Q.N..EQ.E.E...HIT..RR..QTV...P.S.Q.HSEI.L.H.TE.QNQEDQE...L.TTGKIP.LSD
Retrocopy EQMNIREQAE-EPVGHITTIRRHHQTVHRDPTS-QHHSEICLSHRTEPQNQEDQEHWDLRTTGKIPSLSD

Parental  KCLGEKHAVSS
          K.L..KHAVSS
Retrocopy KRLVDKHAVSS

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	3.68 RPM
SRP017611_kidney	0.10 RPM	1.36 RPM
SRP017611_liver	0.00 RPM	0.87 RPM
SRP040447_lung	0.03 RPM	2.09 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.62 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_258 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_258 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
Bos taurus	ENSBTAG00000010774	1 retrocopy	retro_btau_1714,
Canis familiaris	ENSCAFG00000009538	3 retrocopies	retro_cfam_1685, retro_cfam_2137, retro_cfam_578,
Cavia porcellus	ENSCPOG00000020956	1 retrocopy	retro_cpor_258 ,
Myotis lucifugus	ENSMLUG00000009782	1 retrocopy	retro_mluc_389,
Mustela putorius furo	ENSMPUG00000008844	1 retrocopy	retro_mputfur_1626,
Otolemur garnettii	ENSOGAG00000034763	1 retrocopy	retro_ogar_3125,
Tupaia belangeri	ENSTBEG00000014283	1 retrocopy	retro_tbel_4088,