RetrogeneDB ID: retro_cpor_528

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_18:16031082..16032350(-)
• 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_528
GATGGCTTTCTTAAAGAGCTGAACAAGGAGAACTTGCCTCAAATCTCGTCAGAACCTGAAAAGAAGCCAGACCCTGCATT
ATGTACCATAAATAAGCCAAAGAGTAACTCTTATAGTCAAACCAAGAGTCATTTGACTACTAAACAGGTCTTGGGCAAAA
GTGTGGTGAGCAGTGCTGTTCTGAAAGACAGGGTTAATAAGCAGTTTGTTAGAAAAACACAAATTAAGACTCCACCAGTA
AAGTTTCAGCATCTCGCTAAAGGAGTAGAGCTTGCAAGACAAGAAAAACCCTCAAGGACAATTCCCTCTCACATCAGTCA
GACCCTTCATAGGACCCAAGCATCGAAAAAGCCAGTGGTCAAGAACATAAAGGATGTGACGGTTAACAGGAGTAAATATG
AACGACCAAAAGAAAGTCAGGTACAGTCACACACTATTACTGAAGAGAAAGTAAAATACACCAAACCCGGGACATACCCC
AGTTCGCTGCAGGGAGGACCTAACAACAGACATCCAAACAGCAAGCAAGACCAGAAATCCACACAACCTTGTTTTAGGTC
CCAGACACATGAACTGCAAGTCAAAATCCGTAAACCAGAGGCTTAATTTGGCAAATTTCATTCAGTCTTCCCAATGACTC
CTAGCATAAGGACAAATGGAACCAACAGCTTTCAACAAAGAGTGCAGACTGTGGACCTCAAGTTGAAAAAGACTTTTCCC
AGAAGCGTTTCCTGAGCATCACATCTCCCAAAACTCAAGCTAGTGTCACAACCAGAAACAAGAGAGGAGTCCCAGATGAT
ACCCAAACTAATCCAGCCATTAAAAAGACAACAGCAGAGGATCGAAGGAAACTGCTAGAAGAATGGCAGAAATCTAAGGG
GAAAATCTATAAATGGCCTCGTATGGAACTTAAAATAAAAAGTATGGCAGAAATGAATATTTCATTCTGGAAGAACACTG
AAGAAGAGGAAGAAAAGAAAGCACAACTGGAGCTGTCCAACTAGATTAACCCCACCCTGGCAGAATGTTTGAGGTTCCCT
GAAGAGGGGGGGCTTTCTAATGAAATATCTACCATTTTGTCCAACATTCCTGAGGCTGAAAAATTCACTAAATTCTGGTT
CTGCAATGCAAAGCTATTGGCAAGAAAAGACACCTCTGATATTATTGGGCTATATGAAGAAGCCATTAAAAATGGAGCAA
AATCAATTTAAGTGTTATGGGAAGTTGTTCTTAATATTTTGCAAGATCAAAACAGAACTGCAGAGGAA

Alignment

ORF - retro_cpor_528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 57.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGLLKELNKENLLQTLSEPEKKPDPALCTISKPKTNSYNQTKSHLTTKQVLGKSVMSSAVLKDRVNKQFV
          DG.LKELNKENL.Q..SEPEKKPDPALCTI.KPK.NSY.QTKSHLTTKQVLGKSV.SSAVLKDRVNKQFV
Retrocopy DGFLKELNKENLPQISSEPEKKPDPALCTINKPKSNSYSQTKSHLTTKQVLGKSVVSSAVLKDRVNKQFV

Parental  RKTQTRTLPVKLQQLSKGVELARQEKPSRTIPSHFSQTLHRTQASKKPVVKNIKDVMVNRSKYGQPKESQ
          RKTQ..T.PVK.Q.L.KGVELARQEKPSRTIPSH.SQTLHRTQASKKPVVKNIKDV.VNRSKY..PKESQ
Retrocopy RKTQIKTPPVKFQHLAKGVELARQEKPSRTIPSHISQTLHRTQASKKPVVKNIKDVTVNRSKYERPKESQ

Parental  VQSHTVTEEKVKHTKPRTHLSSLQGGPNNRHPNSKQDQKSTQPCFRSQTHELLKSKSENQRPNLKAGNFL
          VQSHT.TEEKVK.TKP.T..SSLQGGPNNRHPNSKQDQKSTQPCFRSQTHEL.........P....G.F.
Retrocopy VQSHTITEEKVKYTKPGTYPSSLQGGPNNRHPNSKQDQKSTQPCFRSQTHEL---QVKIRKPEA*FGKFH

Parental  SVLPMTPSIRTNGTNSFQQRAQTVDPKLKKTFP-QKHFLSKTAPKTQASVTTRNER-VPDDTQTNPTVKK
          SV.PMTPSIRTNGTNSFQQR.QTVD.KLKKTFP.QK.FLS.T.PKTQASVTTRN.R.VPDDTQTNP..KK
Retrocopy SVFPMTPSIRTNGTNSFQQRVQTVDLKLKKTFP<QKRFLSITSPKTQASVTTRNKRGVPDDTQTNPAIKK

Parental  TAAEDRRKQLEEWQKSKGKIYKRPPMELKTKRKVIEEMNISFWKNIEEEEEEKKAQLELSNKINSTLAEC
          T.AEDRRK.LEEWQKSKGKIYK.P.MELK.K.....EMNISFWKN..EEEEEKKAQLELSN.IN.TLAEC
Retrocopy TTAEDRRKLLEEWQKSKGKIYKWPRMELKIKS--MAEMNISFWKN-TEEEEEKKAQLELSN*INPTLAEC

Parental  LRLTEEGVLSNEISTILSNIPEAEKFAKFWICKAKLLARKGTFDVIGLYEEAIKNGAKPIQELREVVLNI
          LR..EEG.LSNEISTILSNIPEAEKF.KFW.C.AKLLARK.T.D.IGLYEEAIKNGAK.I..L.EVVLNI
Retrocopy LRFPEEGGLSNEISTILSNIPEAEKFTKFWFCNAKLLARKDTSDIIGLYEEAIKNGAKSI*VLWEVVLNI

Parental  LQDQNRTAED
          LQDQNRTAE.
Retrocopy LQDQNRTAEE

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_528 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_528 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,