RetrogeneDB ID: retro_cpor_388

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:26029546..26030071(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRCC3
• Ensembl ID: ENSCPOG00000001882
• Aliases: None
• Description: None

Sequence

>retro_cpor_388
CCCATGAGAATTGTGAGTTGGTATCATTCTCATCCTCATATAACCGTTTGGCCCTCTCACGTTGATGTGCACACACAAGC
CACATACCAGATAATGGATCGATGGTTTGTGGGACTTAATTTTTCCTGTTTCATTGAGGATAAAGTCACAAAGACTGGCC
AGATACTCTATACTTGCTTCCAGTCCGTACAGACCCAAGGGAAGTCGGACTATGAAAGAATTGAAATCCCAATTCATATT
GTACCTTGTATCTCCATTGGGAAAGTGTGCTTTGAATCAACAGTAGAGTTGCCCAAGATTCTGTTCCAGGAGGAATGGGA
TGCCTACAGGAGGAATCACAGCCTTAAACATCTGGACTCAGTAACCAAGATCCATAATGGCTCAGTGTTTACCAAGAATC
TGTGCAGTCAGATGTTGGCTGTTAGCAGGCCTCTCCTACAGTGGTTGGAAAATAGAAGAGAGCAAAATCAACAACTACTC
CAGGATTTGAAATAAGAAAAGGAAGACCTTCTGCAAAAACTCTCT

Alignment

ORF - retro_cpor_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.98 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PMRVVGWYHSHPHITVWPSHVADVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSS
          PMR.V.WYHSHPHITVWPSHV.DV.TQA.YQ.MD..FVGL.FSCFIEDK.TKTG..LYTCFQS.Q.Q..S
Retrocopy PMRIVSWYHSHPHITVWPSHV-DVHTQATYQIMDRWFVGLNFSCFIEDKVTKTGQILYTCFQSVQTQGKS

Parental  EYERIEIPIHIIPHVTIGKVCLESAVELPKILCQEEQDAYRRIHSLTHLDSVTKIHNGSVFTKNLCSQMS
          .YERIEIPIHI.P...IGKVC.ES.VELPKIL.QEE.DAYRR.HSL.HLDSVTKIHNGSVFTKNLCSQM.
Retrocopy DYERIEIPIHIVPCISIGKVCFESTVELPKILFQEEWDAYRRNHSLKHLDSVTKIHNGSVFTKNLCSQML

Parental  AVSGPLLQWLEDRLEQNQQHLQELQQEKEELLQELS
          AVS.PLLQWLE.R.EQNQQ.LQ.L..EKE.LLQ.LS
Retrocopy AVSRPLLQWLENRREQNQQLLQDLK*EKEDLLQKLS

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	7.48 RPM
SRP017611_kidney	0.00 RPM	9.00 RPM
SRP017611_liver	0.00 RPM	8.88 RPM
SRP040447_lung	0.00 RPM	9.33 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.92 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_388 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_388 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388 , retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,
Ictidomys tridecemlineatus	ENSSTOG00000019781	2 retrocopies	retro_itri_1271, retro_itri_806,