RetrogeneDB ID: retro_cpor_979

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:8919454..8919845(+)
• Located in intron of: ENSCPOG00000005061

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000013476
• Aliases: None
• Description: None

Sequence

>retro_cpor_979
ATGGGACGCAGGCTGTGGAATGGGCTGTTAGGCCTTGGCCTCTTCGCCCTCGCCCATGCCGCCTTTTCCGCCGCGCAGCA
TCGTTCGTATATGCGATTAACAGAAAATGAAGGCGAAGCGATGCCAATGGACATAGTCCTTCAGACACTTCTGGCCTTCG
CGGTTACCTGTTACAGCATAGTTCACACCGCAGGGGAGTTCAGGGACATCGACACCACGTCGAAACTGAAGAACAAGACA
TGCGACTCCTTAAGGAATCACCCGTCTTTTTACGTATTTAACCATCGTGGCCGAGTACTGTTCCGGCCTTCGGATACAAC
ACATTCTTCACACCAAAATGCACTGACGGCTGATACGGCGCTGAAGTTCACGGAAACTAGAGTCGATACGC

Alignment

ORF - retro_cpor_979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.1 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGIVHIAGEFKDM
          M...LW.GL.G.GLFALAHAAFSAAQHRSYMRLTE.E.E..P.DIVLQTLLAFAVTCY.IVH.AGEF.D.
Retrocopy MGRRLWNGLLGLGLFALAHAAFSAAQHRSYMRLTENEGEAMPMDIVLQTLLAFAVTCYSIVHTAGEFRDI

Parental  DATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDTTNSSNQDALSSNTSLKL-RKLDSLR
          D.TS.LKNKT.D.LRNHPSFYVFNHRGRVLFRPSDTT.SS.Q.AL...T.LK..RKL.S.R
Retrocopy DTTSKLKNKTCDSLRNHPSFYVFNHRGRVLFRPSDTTHSSHQNALTADTALKF>RKLESIR

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	4.89 RPM
SRP017611_kidney	0.00 RPM	4.71 RPM
SRP017611_liver	0.00 RPM	6.40 RPM
SRP040447_lung	0.00 RPM	5.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.23 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_979 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_979 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566, retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171, retro_cpor_979 ,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13,
Oryctolagus cuniculus	ENSOCUG00000029505	1 retrocopy	retro_ocun_660,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224,
Rattus norvegicus	ENSRNOG00000000881	1 retrocopy	retro_rnor_689,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,