RetrogeneDB ID: retro_cpor_229

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_102:3424810..3425915(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000010435
• Aliases: None
• Description: None

Sequence

>retro_cpor_229
AAAAGTCTGGTGCGCAGTGCTGTTCTGAAAGACAAGGTTAATAGACAGTTTGTTAGAAAATACAAAAAGAACTCTACCAA
TAAAGTTACAGCAGCTCTCTAAAGGAGCAGAGCTTACAAAACCAGAAAAACTCCCAAGGACAGTTCCCTCTCACTTCATT
CAAAACCTTCAGAGGACTCAAGCATCAAAGAAACTAGTGGTCATAAAGGATGTAAAAGTTAACAGGAGTAAATATGAACA
ACCAAAGAAACTAAAGTACAGTCACACAGTTACTGGAGAGAAAATAAAACACACCAAACCCATTTGCTGCAGGGAGGATC
TAACAAAAGACATCCAAACAGCAGGCAAGACCAGAAGTGCACACAATCTTGTTTTAGTTCTCAGATGCGTGTACTGCAAA
AACCAAAATCCACAAACCAGAAGCCCCATTTAACATCTGGCAGTTTTCATTCTGCCATTCCAGCCACTCCTGGCATAAGG
GCAAATAGAACCAACAGCTTTCAACAAAGAGCACAGACTGTGGACTTCCCGTTGAGAAAGATTTTTCCCCAGAAGCGTTT
CCTGAGCAACACAGCTCCCAAAACTCAAGCTAATGTCACAACCAAAATTGGGGTTGGAGTCCCAAATTGTACTCAGACTA
CTCCAAACATTAAAAAGACAACAGCAGAAGGTCAAAGGAAACAGTGAGAACTGTAGCCGAAATCTAAGGGGAAAATCTAT
AAATGGCCTTCTATGGAATTTTAAACAAAAAGAAAAGTAATAGAGGAAATGAATACTTCATTCTGGAAGATCACTGAAGA
CAAAGAGGACAGAAAAGGCACAGTGGGAACTGCCTGGTGAGATTAACAGCACTCTAGAATGTCTGAGGCTCACTCTAGAG
GGTGTACTTTCTCATGAAATATTTACCATTTTGTCCAACATTCCTGAGGCTGAAAAGTTTGCTCACCTCTGGATCTGGAA
AGCAAAGCTACTGGAAAGAAAAGGCACCTTTGATGTTTAGGGCCTTACAAACAGGCCAGAGGCCATTAAACATGGAACAA
AACCAACACAAGAGTGGCGGGAAGTTCTTAATGTTTTGCAAGATCAAAACAGAACTGCAAAGGAA

Alignment

ORF - retro_cpor_229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 50.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSVMSSAVLKD-RVNKQFVRKTQTRTLPVKLQQLSKGVELARQEKPSRTIPSHFSQTLHRTQASKKPVVK
          KS...SAVLKD.R........T..RTLP.KLQQLSKG.EL...EK..RT.PSHF.Q.L.RTQASKK.VV.
Retrocopy KSLVRSAVLKD>RLIDSLLENTK-RTLPIKLQQLSKGAELTKPEKLPRTVPSHFIQNLQRTQASKKLVV-

Parental  NIKDVMVNRSKYGQPK-ESQVQSHTVTEEKVKHTKPRTHLSSLQGGPNNRHPNSKQDQKSTQPCFRSQTH
          .IKDV.VNRSKY.QPK.E..VQSH....E...H....THL..LQGG.N.RHPNS.QDQK.TQ.CF.SQ..
Retrocopy -IKDVKVNRSKYEQPK<ETKVQSHSYWRENKTH---QTHL--LQGGSNKRHPNSRQDQKCTQSCFSSQMR

Parental  ELLKSKSENQRPNLKAGNFLSVLPMTPSIRTNGTNSFQQRAQTVDPKLKKTFPQKHFLSKTAPKTQASVT
          .L.K.KS.NQ.P.L..G.F.S..P.TP.IR.N.TNSFQQRAQTVD..L.K.FPQK.FLS.TAPKTQA.VT
Retrocopy VLQKPKSTNQKPHLTSGSFHSAIPATPGIRANRTNSFQQRAQTVDFPLRKIFPQKRFLSNTAPKTQANVT

Parental  TR-NERVPDDTQTNPTVKKTAAEDRRKQLEEWQKSKGKIYKRPPMELKTKRKVIEEMNISFWKNIEEEEE
          T.....VP..TQT.P..KKT.AE..RKQ.E...KSKGKIYK.P.ME..TKRKVIEEMN.SFWK.I.E..E
Retrocopy TKIGVGVPNCTQTTPNIKKTTAEGQRKQ*EL*PKSKGKIYKWPSMEF*TKRKVIEEMNTSFWK-ITEDKE

Parental  EK-KAQLELSNKINSTLAECLRLTEEGVLSNEISTILSNIPEAEKFAKFWICKAKLLARKGTFDVIGLYE
          ...KAQ.EL...INSTL.ECLRLT.EGVLS.EI.TILSNIPEAEKFA..WI.KAKLL.RKGTFDV.GL..
Retrocopy DR>KAQWELPGEINSTL-ECLRLTLEGVLSHEIFTILSNIPEAEKFAHLWIWKAKLLERKGTFDV*GLTN

Parental  --EAIKNGAKPIQELREVVLNILQDQNRTAED
          ..EAIK.G.KP.QE.RE.VLN.LQDQNRTA..
Retrocopy RPEAIKHGTKPTQEWRE-VLNVLQDQNRTAKE

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	0.69 RPM
SRP017611_kidney	0.00 RPM	1.36 RPM
SRP017611_liver	0.00 RPM	0.70 RPM
SRP040447_lung	0.00 RPM	2.77 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.51 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_229 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_229 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007242	1 retrocopy	retro_cfam_858,
Cavia porcellus	ENSCPOG00000010435	2 retrocopies	retro_cpor_229 , retro_cpor_528,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171,
Felis catus	ENSFCAG00000028904	1 retrocopy	retro_fcat_615,
Mustela putorius furo	ENSMPUG00000009729	1 retrocopy	retro_mputfur_1172,
Ochotona princeps	ENSOPRG00000012796	1 retrocopy	retro_opri_904,
Tupaia belangeri	ENSTBEG00000013625	2 retrocopies	retro_tbel_1637, retro_tbel_4436,