RetrogeneDB ID: retro_cpor_3

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_72:3406699..3407920(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025133
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IKZF5
• Ensembl ID: ENSCPOG00000021914
• Aliases: None
• Description: None

Sequence

>retro_cpor_3
ATGGGTGAAAAGAAACCAGAACCTCTGGACTTCGTGAAGGATTTTCAGGAGTACCTGACGCAGCAGACCCATCACGTGAA
CATGATTTCTGGGTCAGTTAGTAAAGACAGAGCCACAGAGGCTTTTCAGGGAGCTGGGCCAGATGGAGATCGAAATGGGC
TGGACCCTCTGTCTGTTGACGTTTCTCCGGATGAAAACTCAGGAACGTTAGTGGACGAGTTTGAAAGGACTCCTGATGGG
AAACTCAAGTGCCGTTACTGCAACTACGCCAGCAGAGGAACAGCTCGGCTCATCGAGCACGTCAGAATCCACACGGGGGA
GAAGCCTCATCGGTGCGACTTATGTCCGTTTGCATCCGCTTACGAGCGCCACCTGGAAGCCCATATTCGTTCCCACACTG
GAGAAAAACCATACAAATGCGAATTATGTTCCTTCCGCTGCAGCGATCAGAGTAATTTGTGCCATCATCGTAGGCGCAAG
CATAAAACGCTGTCGATGAAAGCCAGTAGGTCTTCCTTGAGCAGCAAGAAGATGTGGGGGGGTTCGCAGAAGAAAACGAG
CAATCTGGGGTACTGCAGAAGAGCACTCCTCAATTTAAGCCCACCTTCCATGGTAGTTCAGAAACCGGACTACCTTCATG
ATGTGACCCGTGAAATCCCAAATATCCAGGCCTATGAAAGTATGGCGAAAACTGCATCCCCTACTGGCCTCCCAAGGGAC
CCCCCAAAAGTCATGTTCTCCACTCTAACAGGACAACTGTCCAGCTTGCCACCTGAAGACCAGAAACCTGAATCCCCTGA
TGTAGTTCCTGGACCTGATGAAAAGCATTTCATGATTGAGCGGCCCTCTGCGGTGTGTGCAAGTATTACTCAGAGCCCCT
CTCCTACAAGCCCTGGGCCTGGGCCTCGGCCAGCACACAGTGAGAGGAAGTACAGCCCAGCAGCAGGTTGGAGCACCGAG
CCAAGTGCCCACACCAGTACTCCCATACTAGGAAACAGCCAGCCAAGCACTCTAGCCCCAACCCTGCCAGTGCAGGACCA
TCAGCTTCTGCACCACTGCCCGCACTGTGACATATACTTTGTTGACAATATCCTTTACACGATTCATATAGGATGTCATG
GCTATGAAAACCCTTTTCAGTGTAATATATGTGGATGCAAATGTAAAAACAAATATGATTTCGCCTGCCATTTTGCAAGA
GGGCAACATAACCAACGCTGA

Alignment

ORF - retro_cpor_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 61.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGEKKPEPLDFVKDFQEYLTQQTHHVNMISGSVSGDKEAEALQGAGTDGDQNGLDHPSVEVSLDENSGML
          MGEKKPEPLDFVKDFQEYLTQQTHHVNMISGSVS.D...EA.QGAG.DGD.NGLD..SV.VS.DENSG.L
Retrocopy MGEKKPEPLDFVKDFQEYLTQQTHHVNMISGSVSKDRATEAFQGAGPDGDRNGLDPLSVDVSPDENSGTL

Parental  VDGFERTFDGKLKCRYCNYASKGTARLIEHIRIHTGEKPHRCHLCPFASAYERHLEAHMRSHTGEKPYKC
          VD.FERT.DGKLKCRYCNYAS.GTARLIEH.RIHTGEKPHRC.LCPFASAYERHLEAH.RSHTGEKPYKC
Retrocopy VDEFERTPDGKLKCRYCNYASRGTARLIEHVRIHTGEKPHRCDLCPFASAYERHLEAHIRSHTGEKPYKC

Parental  ELCSFRCSDRSNLSHHRRRKHKMVPIKGTRSSLSSKKMWGVLQKKTSNLGYSRRALINLSPPSMVVQKPD
          ELCSFRCSD.SNL.HHRRRKHK....K..RSSLSSKKMWG..QKKTSNLGY.RRAL.NLSPPSMVVQKPD
Retrocopy ELCSFRCSDQSNLCHHRRRKHKTLSMKASRSSLSSKKMWGGSQKKTSNLGYCRRALLNLSPPSMVVQKPD

Parental  YLNDFTHEIPNIQTDSYESIAKTTPAGGLPRDPQELMVDNPLNQLSTL
          YL.D.T.EIPNIQ...YES.AKT....GLPRDP...M......QLS.L
Retrocopy YLHDVTREIPNIQ--AYESMAKTASPTGLPRDPPKVMFSTLTGQLSSL

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	12.48 RPM
SRP017611_kidney	0.10 RPM	15.07 RPM
SRP017611_liver	0.00 RPM	7.92 RPM
SRP040447_lung	0.00 RPM	14.05 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.13 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_3 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_3 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023847	1 retrocopy	retro_btau_1752,
Cavia porcellus	ENSCPOG00000005792	1 retrocopy	retro_cpor_1135,
Cavia porcellus	ENSCPOG00000021914	1 retrocopy	retro_cpor_3 ,
Mus musculus	ENSMUSG00000040167	1 retrocopy	retro_mmus_2247,
Oryctolagus cuniculus	ENSOCUG00000013340	1 retrocopy	retro_ocun_935,