RetrogeneDB ID: retro_cpor_240

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_107:2778081..2778510(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMFB
• Ensembl ID: ENSCPOG00000004207
• Aliases: None
• Description: None

Sequence

>retro_cpor_240
ACTGAATCTTTGGTGGTTTTTGGTGTCATTGAAGATTCAGTGGAAAAACTGAGAAAGTTTCCTTTTCTCAAAGAAATGAA
CAATGCTGCCATTATAAAGAAGATTGATAGAGATAAATGCCCTCTGGTACTGGATGAGGACCTTGAGGGCACTTCACTAG
ATAAATTTAAAGATGAGCAACCTGAATGACAACCCCACTGGATTGTGCATAGCTATAAATATCCAAGTGACAATGGGCAT
TTTATGTCTTCTATGCTCTGTTTTCCCCAGTCCTGTTGGATGGAAGCCTGGACAATGATGTTGTATGCTGGAAGTAAGAA
TAAGTTAGCTCTAACAGTTGAATTAACCAGGACATTTGAAATAAGAAATACTGAAAACTTCACGGAAGAGTTGACTTCTG
CACTTCTAAAGTATTTCTGCACTAACCTG

Alignment

ORF - retro_cpor_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.18 %
• Parental protein coverage: 94.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SESLVVCDVAEDLVEKLRKFRFRKETNNAAIIMKIDKDKRLVVLDEELEGISPDELKDELPERQPRFIVY
          .ESLVV..V.ED.VEKLRKF.F.KE.NNAAII.KID.DK...VLDE.LEG.S.D..KDE.PE.QP..IV.
Retrocopy TESLVVFGVIEDSVEKLRKFPFLKEMNNAAIIKKIDRDKCPLVLDEDLEGTSLDKFKDEQPE*QPHWIVH

Parental  SYKYQHDDGR-VSYPLCFIFSSPVGCKPEQQMM--YAGSKNKLVQTAELTKVFEIRNTEDLTEEWLRE--
          SYKY..D.G...S..LCF....P..C..E...M..YAGSKNKL..T.ELT..FEIRNTE..TEE......
Retrocopy SYKYPSDNGHFMSSMLCF----PQSCWMEAWTMMLYAGSKNKLALTVELTRTFEIRNTENFTEELTSALL

Parental  KLFSTNV
          K.F.TN.
Retrocopy KYFCTNL

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	0.06 RPM	27.32 RPM
SRP017611_kidney	0.00 RPM	9.63 RPM
SRP017611_liver	0.00 RPM	9.01 RPM
SRP040447_lung	0.00 RPM	14.88 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_240 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_240 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004207	1 retrocopy	retro_cpor_240 ,
Homo sapiens	ENSG00000197045	1 retrocopy	retro_hsap_2818,
Loxodonta africana	ENSLAFG00000004659	1 retrocopy	retro_lafr_493,
Nomascus leucogenys	ENSNLEG00000012717	1 retrocopy	retro_nleu_1197,
Oryctolagus cuniculus	ENSOCUG00000004488	2 retrocopies	retro_ocun_1849, retro_ocun_1881,
Pongo abelii	ENSPPYG00000005830	1 retrocopy	retro_pabe_2209,