RetrogeneDB ID: retro_cpor_1307

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_68:9247748..9248864(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSR1
• Ensembl ID: ENSCPOG00000014833
• Aliases: None
• Description: None

Sequence

>retro_cpor_1307
AAGGTGAGAAAAGAACTCAGCAGAGTAGAACAGAAGCATTGTGCCAGCCAGCTCTGAAACCATAACAAGGAGGCAGTTCT
GGCAGAGAAGAGACAGCTAGCGGCAACTCATCAGGTGCTGGTGGTGCCTTCGTATAACAGAATTTCTTTGTCTGAAGCCC
CTCACTTGCTTCAGCATAGGAACATGAGAACAGTGCTCCTGCAGAAATGGGAGAACACTCAGTGCTTTATGCTGCTGTGC
ATAATTGAAACATTGGTGTTTTTTTTTTTTTTCACATCTGCAAAGCCAGGGCATCTACATACTGTGTTAGACGTGGCTAA
AGTGGTTGATACCATCTTATTCCTCTTTGACCCACTAGAAGACTGGGACAGCACTTGGGATTATCTCTTTTCTGCCTCTG
CTCAGGGCCTCCCTACCTATACACTAGCTGTTCAAGGGGTTTCTGACCTCCCACCTAAGAGGCTGGTAGATTCCAGAAAG
AAGCTAAGTAAAGTAGTGGAGAAGTATTTTCCTGATGATAAACTCTTCCTGTTAGACATTCAGCAAGAGGCAGGGATGCT
GCTTAGGCAGCTGGCTAACCAAAAGCAAAGACATCTTGCTTTTGGAGATTGGCAAGCCTACTTGTTTGCCTATGCTGCGG
ATTTTGTACCTAATGAAGAGAATAACTTGGTGGGCACCTTGAAAATCTCAGGCTATGTGCACAGGCAGACTTTGAATATA
AATAGCTTGCTGCATATCGCTGGAGATGGTGATTTTAAAAAGAAACAGATTGATACCCCTGTGGACCCTTTCCTTTTAAA
TCCTAGAGTGATTAACTCTCAGAAGGATCCAGGCATGACAAAGGAGGTTTGTGCTACAGATGCTGTAGTTGATATGAAAC
ACCTTAAGGTCATGACAAAGGCAGACTCTGACATTCAAGAGTCTTTGCAAACAGAAGTTATCCCAGAACCAGTGGAAGGG
GAGCAATCCTGGCCCACTGAGGAGGAGCTGAATGAGGCAAATGACTTGTTGAAGGAAAGTTTCAAGGTGGTAAAGAAGGT
TCCCAAAGGAACATCCAGTTACCAAGCTTAGTGGATTTTGGATGAAGGCGGTAAAAGTGGTGGGGAAGGAGGTGAC

Alignment

ORF - retro_cpor_1307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.01 %
• Parental protein coverage: 50.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVRRELSRVDQRHRASQLRKQKKEAVLAEKRQLGSKDGAPHQVLVVPLHNRISLLEALHLLQDRNVGTVH
          KVR.ELSRV.Q.H.ASQL....KEAVLAEKRQL.....A.HQVLVVP..NRISL.EA.HLLQ.RN..TV.
Retrocopy KVRKELSRVEQKHCASQL*NHNKEAVLAEKRQLA----ATHQVLVVPSYNRISLSEAPHLLQHRNMRTVL

Parental  VQEWERTHRFMLLC--PQLKHRWFFTSAKPGDLHTVLDMAKVADTILFLLDPLEGWDSTGDYCLSCLFAQ
          .Q.WE.T..FMLLC....L......TSAKPG.LHTVLD.AKV.DTILFL.DPLE.WDST.DY..S...AQ
Retrocopy LQKWENTQCFMLLCIIETLVXXXXXTSAKPGHLHTVLDVAKVVDTILFLFDPLEDWDSTWDYLFSAS-AQ

Parental  GLPTHTLAVQGVSCLPPKKQVDSRKKLSKVVEKRFPDDKLFLLDTQQEAQLLLRQLANQKQRHLAFRDRR
          GLPT.TLAVQGVS.LPPK..VDSRKKLSKVVEK.FPDDKLFLLD.QQEA..LLRQLANQKQRHLAF.D..
Retrocopy GLPTYTLAVQGVSDLPPKRLVDSRKKLSKVVEKYFPDDKLFLLDIQQEAGMLLRQLANQKQRHLAFGDWQ

Parental  AYLFAHAADFVPGEQNKLVGTLKISGYVRGQNLNVNSLLHIVGHGDFQMKQIDAPMDPFPLNPRVIKSLK
          AYLFA.AADFVP.E.N.LVGTLKISGYV..Q.LN.NSLLHI.G.GDF..KQID.P.DPF.LNPRVI.S.K
Retrocopy AYLFAYAADFVPNEENNLVGTLKISGYVHRQTLNINSLLHIAGDGDFKKKQIDTPVDPFLLNPRVINSQK

Parental  DPGMVMEVCTTDAVADMEDLKVLMKADPSRQESLQTEVIPDPMDGEQTWPTEEELSEAKDLLKESSKVVK
          DPGM..EVC.TDAV.DM..LKV..KAD...QESLQTEVIP.P..GEQ.WPTEEEL.EA.DLLKES.KVVK
Retrocopy DPGMTKEVCATDAVVDMKHLKVMTKADSDIQESLQTEVIPEPVEGEQSWPTEEELNEANDLLKESFKVVK

Parental  KVPKGTSSYQAEWILDEGGESDGEGED
          KVPKGTSSYQA.WILDEGG.S.GEG.D
Retrocopy KVPKGTSSYQA*WILDEGGKSGGEGGD

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	25.36 RPM
SRP017611_kidney	0.00 RPM	26.80 RPM
SRP017611_liver	0.00 RPM	16.63 RPM
SRP040447_lung	0.00 RPM	23.56 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1307 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1307 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019273	1 retrocopy	retro_cfam_104,
Cavia porcellus	ENSCPOG00000014833	2 retrocopies	retro_cpor_1258, retro_cpor_1307 ,
Oryctolagus cuniculus	ENSOCUG00000014256	1 retrocopy	retro_ocun_848,