RetrogeneDB ID: retro_cpor_532

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_18:32096423..32096860(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIF1
• Ensembl ID: ENSCPOG00000002068
• Aliases: None
• Description: None

Sequence

>retro_cpor_532
GCCATGAGCCCAAACAGGGATTTACAGGGAGGAAAAGCCTGCAGACTGCTGAAGGCCCAGCAGAAAGACAGGCTGGAGGA
GATCAAGCAGCAACTCCTGGATGGTCCCTAATACAGCCCTGGTGAGGACCGGCCCTCCAAACTGGAAGCCTTCAAGAAGA
AATACGTGGAGTTCAACCTGAATGGAAATGGAGACATCGATATCATGTCCCTGAAGAGAATGCTGCAGAAATTTGGGGTC
CCCAAGACCCACTTAGAGCTAAAGAAATTAATTGGAGAGGTATCTGGTGGCTCTGGGGAGACGTTCAGCTACCTTGACTT
TCTCAGAATGATGCTGGGCAAGCGATCTGCCACCCTGAAAATGATCCTGATGTATGAAGAGAAAGAAAGAGAACAGGAGA
GGCCAACGGCCCCCCAGCCAAGAAAGCTACCTCTGAT

Alignment

ORF - retro_cpor_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMSQTRDFQGGKAFGLLKAQQEERLEEINKQFLDDPKYSTDEDLPSKLEAYKKKYMEFDLNGNGDIDIMS
          AMS..RD.QGGKA..LLKAQQ..RLEEI..Q.LD.P.YS..ED.PSKLEA.KKKY.EF.LNGNGDIDIMS
Retrocopy AMSPNRDLQGGKACRLLKAQQKDRLEEIKQQLLDGP*YSPGEDRPSKLEAFKKKYVEFNLNGNGDIDIMS

Parental  LKRMLEKLGVPKTHLELKKLIGEVSGGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREQEKPT-GPP
          LKRML.K.GVPKTHLELKKLIGEVSGGSGETFSY.DFLRMMLGKRSA.LKMILMYEEK.REQE.PT.GPP
Retrocopy LKRMLQKFGVPKTHLELKKLIGEVSGGSGETFSYLDFLRMMLGKRSATLKMILMYEEKEREQERPT<GPP

Parental  AKKAISE
          AKKA.S.
Retrocopy AKKATSD

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	0.12 RPM	7.53 RPM
SRP017611_kidney	0.10 RPM	18.42 RPM
SRP017611_liver	0.04 RPM	21.46 RPM
SRP040447_lung	0.05 RPM	24.94 RPM
SRP040447_skeletal_muscle	0.03 RPM	0.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_532 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_532 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002068	2 retrocopies	retro_cpor_180, retro_cpor_532 ,