RetrogeneDB ID: retro_cpor_1180

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_53:2036133..2037101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK9
• Ensembl ID: ENSCPOG00000010359
• Aliases: None
• Description: None

Sequence

>retro_cpor_1180
ACCACCAGACCGGTGGCATTGAAGAAGGTACTGATGGAGAACGAGAAGGAAGGGCTCCCATCACCGCCTTGCAGGAGATC
AAGATCCTTCAGCTTCTCAAACATGAGAATGTGGTCAACTTGATTGAGATTTGTCAAACCAAAGCTTCCCTGTATAACCG
CTACCATGGCAGCATATATTTGGTGTTCAACTTCTGCGAGCATGACCTTGCGGGGCTGCTGAGCAACGTCCTAGTCAAGT
TCACGCTGTCTGAGATCAAGAGGGTGATGCAGATGCTGCTCAACGGCCTCTACTACATCCACAGGAACAAGATTCTGCGC
AGGGACATGAAGGCTGCTCATCAGGATGGGGTCCCGAAGCTGGCAGACTTCGGGCTGGCCCCGGCCTTCAGCCTGGCCAA
AAGCAGCCAGCCCAACGGCTACACCAACCGTGTGGTGACGTTCTGGTACTGGCCCCCAGAGCTGCTGCTCGGGCAGCAGA
ACTACAGTCCACCCATTGACCTATGGAGTGCAGAGTGCATCATGGCCAAGATGTGAACCCACAGTCCTATCATGCTGGGC
AACACGGAGCAGCACCAGCTCGCCCTCATCAGCCAGCTCTGTGGCTCCATCACGCCGGAGGTGTGGCCGAATGTGGACAA
GTACGAGCTGTTTGAGAAGCTGGAGCTGGTCAAGGGCCAGAAGTGCATGGTGAAGGACAGGCTGAAGGCCTCCATGCGTG
ACCCCTACGCGCTGGACCTCATTGACAAGCTGCTGGTCCTGGATCCTGCACAGTGCATAGATAGCAACGACGCCCTCAAC
CATGACTTCTTCTGATCTGACCCCGTGCCCTCGGACCTCAAGGGCATGCTGTCCACCCACCTGACGTCCATGTTTGAGTA
CCTGGCACCGCCATGCTGGAAGGGCAGCTAGATCACACAGACCAGAGCCGCAACTTGGCCACCACCAACCAGACAGAGTT
CCAGCGAG

Alignment

ORF - retro_cpor_1180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.42 %
• Parental protein coverage: 67.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGQKVALKKVLMENEKEGFP-ITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHD
          T...VALKKVLMENEKEG.P.ITAL.EIKILQLLKHENVVNLIEIC.TKAS.YNR..GSIYLVF.FCEHD
Retrocopy TTRPVALKKVLMENEKEGLP<ITALQEIKILQLLKHENVVNLIEICQTKASLYNRYHGSIYLVFNFCEHD

Parental  LAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKN
          LAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKIL.RDMKAA......DGV.KLADFGLA.AFSLAK.
Retrocopy LAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILRRDMKAAH----QDGVPKLADFGLAPAFSLAKS

Parental  SQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSIT
          SQPN.YTNRVVT.WY.PPELLLG...Y.PPIDLW.A.CIMA.M.T.SPIM.GNTEQHQLALISQLCGSIT
Retrocopy SQPNGYTNRVVTFWYWPPELLLGQQNYSPPIDLWSAECIMAKM*THSPIMLGNTEQHQLALISQLCGSIT

Parental  PEVWPNVDKYELFEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDP
          PEVWPNVDKYELFEKLELVKGQK..VKDRLKA..RDPYALDLIDKLLVLDPAQ.IDS.DALNHDFF.SDP
Retrocopy PEVWPNVDKYELFEKLELVKGQKCMVKDRLKASMRDPYALDLIDKLLVLDPAQCIDSNDALNHDFF*SDP

Parental  MPSDLKGMLSTHLTSMFEYLAPPRRKGSQITQQTTNQSRNPATTNQTEFE
          .PSDLKGMLSTHLTSMFEYLAPP..KGS.ITQ..T.....P..T.Q...E
Retrocopy VPSDLKGMLSTHLTSMFEYLAPPCWKGS*ITQ--TRAATWPPPTRQSSSE

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	60.79 RPM
SRP017611_kidney	0.00 RPM	35.28 RPM
SRP017611_liver	0.00 RPM	23.90 RPM
SRP040447_lung	0.08 RPM	75.71 RPM
SRP040447_skeletal_muscle	0.01 RPM	22.42 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1180 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1180 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000010359	1 retrocopy	retro_cpor_1180 ,