RetrogeneDB ID: retro_cpor_1258

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_60:15165..16272(+)
• Located in intron of: ENSCPOG00000022358

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_1258
AAGGTGAGAAAAGAACTCAGCAGAGTAGAACAGAAGCATTGTGCCAGCCAGCTCTGAAACCATAACAAGGAGGCAGTTCT
GGCAGAGAAGAGACAGCTAGCAGCAACTCATCAGGTGCTGGTGGTGCCTTCGTATAACAGAATTTCTTTGTCTGAAGCCC
CTCACTTGCTTCAGCATAGGAACATGAGAACAGTGCTCCTGCAGAAATGGGAGAACACTCAGTGCTTTATGCTGCTGTGC
CTAATTGAAACATTGGTGTTTTTTTTACATCTGCAAAGCCAGGGCATCTGCATACTGTGTTAGACATGGGTAAAGTGGTT
GACACCATCTTATTCCTCTTTGATCCACTAGAAGGCTGGGACAGCACTTGGGATTATCCCTTTTCTGCCTCTGCTTAGGC
CTCCCTACCTATACACTAGCTGTTCAAGGGGTTTCTGACCTCCCACCTAAGAGGCTGGTAGATTCCAGAAAGAAGCTAAG
TAAAGTAGTGGAAAGTATTTTCCTGATGATAAACTCTTCCTGTTAGACATTCAGCAGGAGGCAGGGATGCTGCTTAGGCA
GCTGGCTAACCAAAAGCAAAGACATCTTGCTTTTGGAGATTGGCAAGCCTACTTGTTTGTCTATGCTGCGGATTTTGTGC
CCAAGGAAGAGAATAACTTGGTGGGCACTTTGAAAATCTCAGGCTATGTGCACAGGCAGACTTTGAATATAAATAGCTTG
CTGTATATCTCTGGACATGATGATTTTCAAAAGAAACAAATTGATACCCCTATGGATCCTTTCCTTTTAAATCCTAGAGT
TATTAACTCTCAGAAGGATCCAGGCATGACAAAGGAGGTTTGTGCTACAGATGCTGTAGCTGATATGAAACACCTTAAGG
TCATGACAAAGGCAGACTCTAACAGACAAGAGTCTTTGCAAACAGAAGTTATCCCAGAACCAGTGGAAGGGGAGAAATCC
TGGCCCACTGAGGAGGAGCTGAATGAGGCAAATGACTTGTTGAAGGAAAGTTTCAAGGTGGTAAAGAAGGTTCCCAAAGG
AACATCCAGTTACCAAGCTTAGTGGATTTTGGATGAAGGCGGTAAAAGTGGTGGGGAAGGAGATGAC

Alignment

ORF - retro_cpor_1258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.34 %
• Parental protein coverage: 50.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

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-PQLKHRWFFTSAKPGDLHTVLDMAKVADTILFLLDPLEGWDSTGDYCLS-CLFAQ
          .Q.WE.T..FMLLC.P........TSAKPG.LHTVLDM.KV.DTILFL.DPLEGWDST.DY..S.CL...
Retrocopy LQKWENTQCFMLLC<PN*NIGXXXTSAKPGHLHTVLDMGKVVDTILFLFDPLEGWDSTWDYPFS<CL-CL

Parental  GLPTHTLAVQGVSCLPPKKQVDSRKKLSKVVE-KRFPDDKLFLLDTQQEAQLLLRQLANQKQRHLAFRDR
          GLPT.TLAVQGVS.LPPK..VDSRKKLSKVVE.K.FPDDKLFLLD.QQEA..LLRQLANQKQRHLAF.D.
Retrocopy GLPTYTLAVQGVSDLPPKRLVDSRKKLSKVVE<KYFPDDKLFLLDIQQEAGMLLRQLANQKQRHLAFGDW

Parental  RAYLFAHAADFVPGEQNKLVGTLKISGYVRGQNLNVNSLLHIVGHGDFQMKQIDAPMDPFPLNPRVIKSL
          .AYLF..AADFVP.E.N.LVGTLKISGYV..Q.LN.NSLL.I.GH.DFQ.KQID.PMDPF.LNPRVI.S.
Retrocopy QAYLFVYAADFVPKEENNLVGTLKISGYVHRQTLNINSLLYISGHDDFQKKQIDTPMDPFLLNPRVINSQ

Parental  KDPGMVMEVCTTDAVADMEDLKVLMKADPSRQESLQTEVIPDPMDGEQTWPTEEELSEAKDLLKESSKVV
          KDPGM..EVC.TDAVADM..LKV..KAD..RQESLQTEVIP.P..GE..WPTEEEL.EA.DLLKES.KVV
Retrocopy KDPGMTKEVCATDAVADMKHLKVMTKADSNRQESLQTEVIPEPVEGEKSWPTEEELNEANDLLKESFKVV

Parental  KKVPKGTSSYQAEWILDEGGESDGEGED
          KKVPKGTSSYQA.WILDEGG.S.GEG.D
Retrocopy KKVPKGTSSYQA*WILDEGGKSGGEGDD

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	0.04 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_1258 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1258 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,