RetrogeneDB ID: retro_cpor_1220

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_59:4359444..4360002(+)
• Located in intron of: ENSCPOG00000006171

Retrocopy information

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

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSCPOG00000020809
• Aliases: None
• Description: None

Sequence

>retro_cpor_1220
TCGAGTGAGGAAAGAGCCCTCGACGCGGAGCTTCTCGCCGAGAACGCGAACGAAAACTCGCCTCCGGATTATTCTGAATA
CATGACGGGGAAAAAAATTCCCCCTGAAGGAATTCCCGGCATTGACCTCTCCGATCCCAAACAGTTGGCCGAATTCACCA
GAGTGAAGCGCAAAAGAGGCAAGGATGATGTTCCCAGGACTGTCGCTTGCCGCCAAGAAGGCTGCAAAAAGATGTTCAAG
GACAACTGCGCCATGAGGAAGCATCTGCACACCCATGGCCCCAGAGTCCACATCTGCTCCGAATGCGGCAAAGCTTTTCT
GGAGAACTCAAAACTGAAACGACACCAGTTGGTTCACACCGGAGAGAGGCCCTTCCAGTGCAAGTTTGAAGGCTGCGGGA
AATCCTTTTCCCTAGGTTTCAATTTGCGCACTCATATGCGAATTCACACTGGAGACCGACCTTTCGTGTGTCCTTTCACT
GGCTGTAATAGAAGGTTTGCACAGTCAACTAACCTGAAGTCCCATATCTTAGCCCATGCTAAGAACAAGAACAGCCAG

Alignment

ORF - retro_cpor_1220 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADEKKDIDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRT
          ..E....D.E...E.....ENSPPDYSEYMTGKK.PP.GIPGIDLSDPKQLAEF.R.K.RK...DD.PRT
Retrocopy SSEERALDAELLAENA--NENSPPDYSEYMTGKKIPPEGIPGIDLSDPKQLAEFTRVK-RKRGKDDVPRT

Parental  IACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFS
          .AC...GC.KMF.DN.AMRKHLHTHGPRVH.C.ECGKAF.E.SKLKRHQLVHTGE.PFQC.FEGCGK.FS
Retrocopy VACRQEGCKKMFKDNCAMRKHLHTHGPRVHICSECGKAFLENSKLKRHQLVHTGERPFQCKFEGCGKSFS

Parental  LDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ
          L.FNLRTH.RIHTGDRP.VCPF.GCN..FAQSTNLKSHIL.HAK.KN.Q
Retrocopy LGFNLRTHMRIHTGDRPFVCPFTGCNRRFAQSTNLKSHILAHAKNKNSQ

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	23.18 RPM
SRP017611_kidney	0.00 RPM	29.21 RPM
SRP017611_liver	0.04 RPM	20.76 RPM
SRP040447_lung	0.08 RPM	29.74 RPM
SRP040447_skeletal_muscle	0.01 RPM	15.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1220 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1220 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220 , retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,