RetrogeneDB ID: retro_cpor_907

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_33:577728..580475(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000004210
• Aliases: None
• Description: DNA ligase [Source:UniProtKB/TrEMBL;Acc:H0V2M3]

Sequence

>retro_cpor_907
CAGTGGAGTATCATGTCATTTTTCTACCCCACCAAAGAGGGTAAAGCAAAGAAGCCTGAGAAGGAAACCAACAGGAGCAG
CGGCAGAGAGACAGAGCCCCCTCCAAAGGTGGCACTGAGGGAGCGGAATGGAGTGGTGCCTGATAGTGACTCTCCAGTGA
AGAGGTCAGGGAGGAAGGCCGTGCGCGTCTTGAGCAGCGAAGCAGAGGAAAAAGATGAAGCCCTCAGCCCCACTGAAGAC
CAGAAGCCTGGGTCAGATTCCCCACAGGGGTCCCCGCCCAACCTCACCACGTGTCCCGGAAACAGCCCTCCCTTCTCGGA
CACTTCCCCTATGGTCGTCTCCCCATCAGGACTACCAAAGCGTCTCACAGCTTGGAAACAGCTCCCGAAACGGGTAATTC
AGGATGTGTTGGAGGATCAGAATGAGGACAAAGACAGAGAAGCTAAGAAGAGGAAGGAGGAAAAAGAAGCAGAGACTCCA
AGAGAAAGCCCAACAGAGACTGGAGCGGCAACAACGAAGGAAGAAGAGGAGGGGATCAGCCCTCGACACCCCCTGAGCCC
CCAGAACCCCAAAAGCAGAAGCCCCAGCAAAGACAGAAGGTGTTTCCACACCCAAGCTCCCCAGAAGCAGCAGCCACAGG
TAAAGAACCAGAGCAAGGCTGCCCCCAGAGTCTCCAGGACCCTCAGCAGTTTCTTCACAACCCGGAAGCCATCAGTCAAA
ACCCATGTGAAAGAAGAGCAGTCAGGTACCGCGGGAAAAGAGGGGGCCAAGGGATCCCTGGGCCCAGTGAGCTACAATCC
TGCTAAGAACAACTACCACCCCATGGAGTATGCCTGCTGGAGACAGGGCAGAAGGTTCCTTCCCTGGCTGTGGCACCGAC
GTTTGAGAAGATTGAGGAGGTTTCTGCTGGGCTCCGGATGGTGGAGACGCTGAGCAACTTGCTGCCCTCTGTGGTGGCCC
TGTCCCCTCCAGACCTGCTCCCTGTCCTCTACCTCACCCTTAACCGCCTTGGGCCTCCCCAGCAGGGCCTAGAGCTTGGC
GTTGGTGATGGTGTCCTTCTCAAGGCCGTGGCCCAGGCCACAGGCCACCATCTGGAATCTGTCCGGGCTGAGGCTGTTGA
GAGGGGAGACATTGGGCTGGTGGCTGAGAACAGCCGCAGTACTCAGAGACTGATGCTGCCACCACCTCCTCTTACCGCTT
CTGGGGTCTTCTCCAAGTTCCAGGACATTGCCCGGCTCACCGGCAATGCTTCCATGACCAAGAAGATGGCTATCATCAAA
GGCTGCTTTGTTGTCTGCCGCCACTCAGAAGCCCCGTTCATCGCCAGGGCCCTGAGTGGACGGCTGCGCCTCGGGTTGGC
CAAGCAGTCGGTGCTGGCTGCCCTTTCCCAGGCTGCGAGCCAAGAATTCCCAGGCCAAGAATTCCCTCTGGCCATGGTGG
ATGATGGGACAGGCAAGACCACAGAGGCCAGAAAGACATGGCTAGAGGAGCAAGGCATGATCTTGAAGCAGACATTCTGC
GAGGTGCCTGACCTGGACCGAATCATCCCTATGCTGCTGGAGCATGGCTTGGAGCGACTCCCAGAGCACTGCAGGCTGAG
CCCAGGGGTCCCTCTGAAACCTATGTTGGCCCATCCCACTCGGGGTGTCAGTGATGTCCTGAATCGCTTTGAGGAGGCAG
CCTTTACCTGCAAGTACAAATACGATGGGTAGAGGGCACAGATCCATCTTCTAGAAGGTGGGGAGGTGAAGATCTTCAGC
AGGAATCAGGAAGACAACATGGGGAAGTACCCCGACATCATCAGCCGCATCCCCAAGATTAAACTCCCCTCAGTCACATC
CTTTATCCTGGACATGAAGCTGTGGCTTGGGACCGGGAAAAAAAGCAGATCCAGCCATTACAAGTGCTAACCACTTGCAA
ACGGAAAGAAGTAGACACTGCAGAAATCCAGGTGCAGGTGTGTCCATGTGCCTTTGACCTCATCTACCTCAGTGGAGAGT
CTTTGGTCCCTGAGCCCCTGTCCCAACGCCGGCAGCTGCTCCGGGAGAACTTCGTAGAGACAGAAGGCGAGTTTGTCTTC
GCCACCTCTCTGGACACCAAGGACATGGAGCAGATTGCTGAGTTCTTGGAACAGTCAGTGAAAGACTCCTGCGAGGGGCT
GATGGTAAAGACCTTGGATGCTGATGCCACCTATGAGATTGCCAAGAGGTCACACAACTGGCTCAAGCTGAAGAAGGACT
ACCTCGATGGAATGGGTGACACCCTAGACCTCGTGGTGATAGGCACCTACCTGGGCCAGGGAAAGTGGACCAGCCACTAT
GGGGGCTTCCTGCTGGCTGCCTATGATGAGGAGAGCGAGGAGCTACAGGCCATATGCAACCTCGGAACGGGCTTCAGCAA
TGAGCAGCTGGAAGAGCATTACCAGAGCCTGGAGGCCCTGGTGCTTCCCACCCACGCCCCCACGTGCGGGCAGATGGTGC
CTTGGCGCCTGACCACTGGTTGGACCCCAATACTGTGTGGGAGGTGAAGTGTGCCATCTCTGTCTCTCCCCCATCTACCC
TGTTGCCCAGGGCCTGGTGGACAGTGAAAAGGGGCTCTCCCTCCACTTCCCTCGGTTTATTCGCGTACATGAGGACAAGA
AGCCAGAGGAGGCCACTACCAGTGCGTAGGCGGCCTGTCTGTACCACAAGCAAAGTCAGATTCAGAACCAAGGCATTGAC
TCAGACTCTGATGATGTAGAGTTCTAC

Alignment

ORF - retro_cpor_907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.0 %
• Parental protein coverage: 99.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QRSIMSFFYPTKEGKAKKPEKDTNKSSGRETEPPPKVALKERNGVVPDNDSPVKRSGRKAAQVLSSEGEE
          Q.SIMSFFYPTKEGKAKKPEK.TN.SSGRETEPPPKVAL.ERNGVVPD.DSPVKRSGRKA..VLSSE.EE
Retrocopy QWSIMSFFYPTKEGKAKKPEKETNRSSGRETEPPPKVALRERNGVVPDSDSPVKRSGRKAVRVLSSEAEE

Parental  EDEALSPSEDQKPEPDSPQGSPPNLAKCPKNSPSFSDTSPMDISSSGIPKRITARKQLPKRVIQDVLEDQ
          .DEALSP.EDQKP..DSPQGSPPNL..CP.NSP.FSDTSPM..S.SG.PKR.TA.KQLPKRVIQDVLEDQ
Retrocopy KDEALSPTEDQKPGSDSPQGSPPNLTTCPGNSPPFSDTSPMVVSPSGLPKRLTAWKQLPKRVIQDVLEDQ

Parental  NEDKDREAKKRKEEKEAETPRESLVETGAATVKEEEEG-HQPSTPPEPP-KAPKAEAPAKTEGVSTPKVP
          NEDKDREAKKRKEEKEAETPRES..ETGAAT.KEEEEG..QPSTPPEPP...PKAEAPAKTEGVSTPK.P
Retrocopy NEDKDREAKKRKEEKEAETPRESPTETGAATTKEEEEG<DQPSTPPEPP<RTPKAEAPAKTEGVSTPKLP

Parental  -QKQEPQEKNQSKAAPRVSRNLSSFFTPRKPSVKTDVKQEQSGTPGKEEAKRSLDPVSYNPAKNNYHPIE
          .QKQ.PQ.KNQSKAAPRVSR.LSSFFT.RKPSVKT.VK.EQSGT.GKE.AK.SL.PVSYNPAKNNYHP.E
Retrocopy <QKQQPQVKNQSKAAPRVSRTLSSFFTTRKPSVKTHVKEEQSGTAGKEGAKGSLGPVSYNPAKNNYHPME

Parental  DACWRQG-QKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLTLNRLGPPQQGLE
          .ACWRQG.QKVP.LAVA.TFEKIEEVSA.LRMVETLSNLL.SVVALSPPDLLPVLYLTLNRLGPPQQGLE
Retrocopy YACWRQG<QKVPSLAVAPTFEKIEEVSAGLRMVETLSNLLPSVVALSPPDLLPVLYLTLNRLGPPQQGLE

Parental  LGVGDGVLLKAVAQATGRQLESVRAEAVEKGDIGLVAENSRSTQRLMLPPPPLTTSGVFSKFRDIARLTG
          LGVGDGVLLKAVAQATG..LESVRAEAVE.GDIGLVAENSRSTQRLMLPPPPLT.SGVFSKF.DIARLTG
Retrocopy LGVGDGVLLKAVAQATGHHLESVRAEAVERGDIGLVAENSRSTQRLMLPPPPLTASGVFSKFQDIARLTG

Parental  NASMTKKMDIIKGLFVACRHSEARFIARALSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAVVDAGKG
          NASMTKKM.IIKG.FV.CRHSEA.FIARALSGRLRLGLA.QSVLAALSQA.S...PGQEFP.A.VD.G.G
Retrocopy NASMTKKMAIIKGCFVVCRHSEAPFIARALSGRLRLGLAKQSVLAALSQAASQEFPGQEFPLAMVDDGTG

Parental  KTTEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVSEVLK
          KTTEARKTWLEEQGMILKQTFCEVPDLDRIIP.LLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVS.VL.
Retrocopy KTTEARKTWLEEQGMILKQTFCEVPDLDRIIPMLLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVSDVLN

Parental  RFEETAFTCEYKYDGQRAQIHLLEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDT-EAVAW
          RFEE.AFTC.YKYDG.RAQIHLLEGGEVKIFSRNQEDN.GKYPDIISRIPKIKLPSVTSFILD..EAVAW
Retrocopy RFEEAAFTCKYKYDG*RAQIHLLEGGEVKIFSRNQEDNMGKYPDIISRIPKIKLPSVTSFILDM<EAVAW

Parental  DREKKQIQPFQVLTTRKRKEVDAAEIQVQVCLYAFDLIYLNGESLVREPLSQRRQLLRENFVETEGEFVF
          DREKKQIQP.QVLTT.KRKEVD.AEIQVQVC..AFDLIYL.GESLV.EPLSQRRQLLRENFVETEGEFVF
Retrocopy DREKKQIQPLQVLTTCKRKEVDTAEIQVQVCPCAFDLIYLSGESLVPEPLSQRRQLLRENFVETEGEFVF

Parental  ATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAY
          ATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLD.DATYEIAKRSHNWLKLKKDYLDG.GDTLDLVVIG.Y
Retrocopy ATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLDADATYEIAKRSHNWLKLKKDYLDGMGDTLDLVVIGTY

Parental  LGRGKRAGRYGGFLLAAYDEESEELQAICKLGTGFSDEQLEEHYQSLQALVLPT-PRPYVRADGAVAPDH
          LG.GK....YGGFLLAAYDEESEELQAIC.LGTGFS.EQLEEHYQSL.ALVLPT.PRP.VRADGA.APDH
Retrocopy LGQGKWTSHYGGFLLAAYDEESEELQAICNLGTGFSNEQLEEHYQSLEALVLPT<PRPHVRADGALAPDH

Parental  WLDPSAVWEVKCA-DLSLSPIYPAARGLVDSEKGISLRFPRFIRVREDKKPEEATTSAQVACLYRKQSQI
          WLDP..VWEVKCA..L.LSPIYP.A.GLVDSEKG.SL.FPRFIRV.EDKKPEEATTSA..ACLY.KQSQI
Retrocopy WLDPNTVWEVKCA<HLCLSPIYPVAQGLVDSEKGLSLHFPRFIRVHEDKKPEEATTSA*AACLYHKQSQI

Parental  QNQGIDSDSDDEEFY
          QNQGIDSDSDD.EFY
Retrocopy QNQGIDSDSDDVEFY

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	27.09 RPM
SRP017611_kidney	0.00 RPM	74.33 RPM
SRP017611_liver	0.00 RPM	32.73 RPM
SRP040447_lung	0.10 RPM	45.83 RPM
SRP040447_skeletal_muscle	0.00 RPM	24.79 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_907 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_907 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004210	2 retrocopies	retro_cpor_907 , retro_cpor_914,