RetrogeneDB ID: retro_cpor_914

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_33:647636..650386(-)
• 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_914
ATGCAGTGGAGTATCATGTCATTTTTCTACCCCACCAAAGAGGGTAAAGCAAAGAAGACTGAGAAGGAAACCAACAGGAG
CAGCGGCAGAGAGACAGAGCCCCCTCCAAAGGTGGCACTGAGGGAGCGGAATGGAGTGGTGCCTGATAGTGACTCTCCAG
TGAAGAGGTCAGGGAGGAAGGCCGTGCGCGTCTTGAGCAGCGAAGCAGAGGAAAAAGATGAAGCCCTCAGCCCCACTGAA
GACCAGAAGCCTGGGTCAGATTCCCCACAGGGGTCCCCGCCCAACCTCACCACGTGTCCCGGAAACAGCCCTCCCTTCTC
GGACACTTCCCCTATGGTCGTCTCCCCATCAGGACTACCAAAGCGTCTCACAGCTTGGAAACAGCTCCCGAAACGGGTAA
TTCAGGATGTGTTGGAGGATCAGAATGAGGACAAAGACAGAGAAGCTAAGAAGAGGAAGGAGGAAAAAGAAGCAGAGACT
CCAAGAGAAAGCCCAACAGAGACTGGAGCGGCAACAACGAAGGAAGAAGAGGAGGGGATCAGCCCTCGACACCCCCTGAG
CCCCCAGAACCCCAAAAGCAGAAGCCCCAGCAAAGACAGAAGGTGTTTCCACACCCAAGCTCCCCAGAAGCAGCAGCCAC
AGGTAAAGAACCAGAGCAAGGCTGCCCCCAGAGTCTCCAGGACCCTCAGCAGTTTCTTCACAACCCGGAAGCCATCAGTC
AAAACCCATGTGAAAGAAGAGCAGTCAGGTACCGCGGGAAAAGAGGGGGCCAAGGGATCCCTGGGCCCAGTGAGCTACAA
TCCTGCTAAGAACAACTACCACCCCATGGAGTATGCCTGCTGGAGACAGGGCAGAAGGTTCCTTCCCTGGCTGTGGCACC
GACGTTTGAGAAGATTGAGGAGGTTTCTGCTGGGCTCTGGATGGTGGAAACGCTGAGCAACTTGCTGCCCTCTGTGGTGG
CCCTGTCCCCTCCAGACCTGCTCCCTGTCCTCTACCTCACCCTTAACTGCCTTGGGCCTCCCCAGCAGGGCCTAGAGCTT
GGCGTTGGTGATGGTGTCCTTCTCAAGGCCGTGGCCCAGGCCACAGGCCACCATCTGGAATCTGTCCGGGCTGAGGCTGT
TGAGAGGGGAGACATTGGGCTGGTGGCTGAGAACAGCCGCAGTACTCAGAGACTGATGCTGCCACCACCTCCTCTTACCG
CTTCTGGGGTCTTCTCCAAGTTCCAGGACATTGCCCGGCTCACCGGCAATGCTTCCATGACCAAGAAGATGGCTATCATC
AAAGGCTGCTTTGTTGTCTGCCGCCACTCAGAAGCCCCGTTCATCACCAGGGCCCTGAGTGGACGGCTGCGCCTCGGGTT
GGCCAAGCAGTCGGTGCTGGCTGCCCTTTCCCAGGCTGCGAGCCAAGAATTCCCAGGCCAAGAATTCCCTCTGGCCATGG
TGGATGATGGGACAGGCAAGACCACAGAGGCCAGAAAGACATGGCTAGAGGAGCAAGGCATGATCTTGAAGCAGACATTC
TGCGAGGTGCCTGACCTGGACCGAATCATCCCTATGCTGCTGGAGCATGGCTTGGAGCGACTCCCAGAGCACTGCAGGCT
GAGCCCAGGGGTCCCTCTGAAACCTATGTTGGCCCATCCCACTCGGGGTGTCAGTGATGTCCTGAAACGCTTTGAGGAGG
CAGCCTTTACCTGCAAGTACAAATACGATGGGTAGAGGGCACAGATCCATCTTCTAGAAGGTGGGGAGGTGAAGATCTTC
AGCAGGAATCAGGAAGACAACATGGGGAAGTACCCCGACATCATCAGCCGCATCCCCAAGATTAAACTCCCCTCAGTCAC
ATCCTTTATCCTGGACATGAAGCTGTGGCTTGGGACCGGGAAAAAAAGCAGATCCAGCCATTACAAGTGCTAACCACTCG
CAAACGGAAAGAAGTAGACACTGCAGAAATCCAGGTGCAGGTGTGTCCATGTGCCTTTGACCTCATCTACCTCAGTGGAG
AGTCTTTGGTCCGTGAGCCCCTGTCCCAATGCCAGCAGCTGCTCTGGGAGAACGTTGTAGAGACAGAAGGCGAGTTTGTC
TTCGCCACCTCTCTGGACACCAAGGACATGGAGCAGATTGCTGAGTTCTTGGAACAGTCAGTGAAAGACTCCTGCGAGGG
GCTGATGGTAAAGACCTTGGATGCTGATGCCACCTATGAGATTGCCAAGAGGTCACACAACTGGCTCAAGCTGAAGAAGG
ACTACCTCGATGGCATGGGTGACACCCTAGACCTCGTGGTGATAGGCACCTACCTGGGCCAGGGAAAGTGGACCAGCCAC
TATGGGGGCTTCCTGCTGGCTGCCTATGATGAGGAGAGCGAGGAGCTACAGGCCATATGCAACCTCGGAACGGGCTTCAG
CAATGAGCAGCTGGAAGAGCATTACCAGAGCCTGGAGGCCCTGGTGCTTCCCACCCACGCCCCCACGTGCGGGCAGATGG
TGCCTTGGCGCCTGACCACTGGTTGGACCCCAATACTGTGTGGGAGGTGAAGTGTGCCATCTCTGTCTCTCCCCCATCTA
CCCTGTTGCCCAGGGCCTGGTCGACAGTGAAAAGGGGCTCTCCCTCCACTTCCCTCGGTTTATTCGCGTACATGAGGACA
AGAAGCCAGAGGAGGCCACTACCAGTGCGTAGGCGGCCTGTCTGTACCACAAGCAAAGTCAGATTCAGAACCAAGGCATT
GACTCAGACTCTGATGATGTAGAGTTCTAC

Alignment

ORF - retro_cpor_914 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.47 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MQRSIMSFFYPTKEGKAKKPEKDTNKSSGRETEPPPKVALKERNGVVPDNDSPVKRSGRKAAQVLSSEGE
          MQ.SIMSFFYPTKEGKAKK.EK.TN.SSGRETEPPPKVAL.ERNGVVPD.DSPVKRSGRKA..VLSSE.E
Retrocopy MQWSIMSFFYPTKEGKAKKTEKETNRSSGRETEPPPKVALRERNGVVPDSDSPVKRSGRKAVRVLSSEAE

Parental  EEDEALSPSEDQKPEPDSPQGSPPNLAKCPKNSPSFSDTSPMDISSSGIPKRITARKQLPKRVIQDVLED
          E.DEALSP.EDQKP..DSPQGSPPNL..CP.NSP.FSDTSPM..S.SG.PKR.TA.KQLPKRVIQDVLED
Retrocopy EKDEALSPTEDQKPGSDSPQGSPPNLTTCPGNSPPFSDTSPMVVSPSGLPKRLTAWKQLPKRVIQDVLED

Parental  QNEDKDREAKKRKEEKEAETPRESLVETGAATVKEEEEG-HQPSTPPEPP-KAPKAEAPAKTEGVSTPKV
          QNEDKDREAKKRKEEKEAETPRES..ETGAAT.KEEEEG..QPSTPPEPP...PKAEAPAKTEGVSTPK.
Retrocopy QNEDKDREAKKRKEEKEAETPRESPTETGAATTKEEEEG<DQPSTPPEPP<RTPKAEAPAKTEGVSTPKL

Parental  P-QKQEPQEKNQSKAAPRVSRNLSSFFTPRKPSVKTDVKQEQSGTPGKEEAKRSLDPVSYNPAKNNYHPI
          P.QKQ.PQ.KNQSKAAPRVSR.LSSFFT.RKPSVKT.VK.EQSGT.GKE.AK.SL.PVSYNPAKNNYHP.
Retrocopy P<QKQQPQVKNQSKAAPRVSRTLSSFFTTRKPSVKTHVKEEQSGTAGKEGAKGSLGPVSYNPAKNNYHPM

Parental  EDACWRQG-QKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLTLNRLGPPQQGL
          E.ACWRQG.QKVP.LAVA.TFEKIEEVSA.L.MVETLSNLL.SVVALSPPDLLPVLYLTLN.LGPPQQGL
Retrocopy EYACWRQG<QKVPSLAVAPTFEKIEEVSAGLWMVETLSNLLPSVVALSPPDLLPVLYLTLNCLGPPQQGL

Parental  ELGVGDGVLLKAVAQATGRQLESVRAEAVEKGDIGLVAENSRSTQRLMLPPPPLTTSGVFSKFRDIARLT
          ELGVGDGVLLKAVAQATG..LESVRAEAVE.GDIGLVAENSRSTQRLMLPPPPLT.SGVFSKF.DIARLT
Retrocopy ELGVGDGVLLKAVAQATGHHLESVRAEAVERGDIGLVAENSRSTQRLMLPPPPLTASGVFSKFQDIARLT

Parental  GNASMTKKMDIIKGLFVACRHSEARFIARALSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAVVDAGK
          GNASMTKKM.IIKG.FV.CRHSEA.FI.RALSGRLRLGLA.QSVLAALSQA.S...PGQEFP.A.VD.G.
Retrocopy GNASMTKKMAIIKGCFVVCRHSEAPFITRALSGRLRLGLAKQSVLAALSQAASQEFPGQEFPLAMVDDGT

Parental  GKTTEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVSEVL
          GKTTEARKTWLEEQGMILKQTFCEVPDLDRIIP.LLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVS.VL
Retrocopy GKTTEARKTWLEEQGMILKQTFCEVPDLDRIIPMLLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVSDVL

Parental  KRFEETAFTCEYKYDGQRAQIHLLEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDT-EAVA
          KRFEE.AFTC.YKYDG.RAQIHLLEGGEVKIFSRNQEDN.GKYPDIISRIPKIKLPSVTSFILD..EAVA
Retrocopy KRFEEAAFTCKYKYDG*RAQIHLLEGGEVKIFSRNQEDNMGKYPDIISRIPKIKLPSVTSFILDM<EAVA

Parental  WDREKKQIQPFQVLTTRKRKEVDAAEIQVQVCLYAFDLIYLNGESLVREPLSQRRQLLRENFVETEGEFV
          WDREKKQIQP.QVLTTRKRKEVD.AEIQVQVC..AFDLIYL.GESLVREPLSQ..QLL.EN.VETEGEFV
Retrocopy WDREKKQIQPLQVLTTRKRKEVDTAEIQVQVCPCAFDLIYLSGESLVREPLSQCQQLLWENVVETEGEFV

Parental  FATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGA
          FATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLD.DATYEIAKRSHNWLKLKKDYLDG.GDTLDLVVIG.
Retrocopy FATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLDADATYEIAKRSHNWLKLKKDYLDGMGDTLDLVVIGT

Parental  YLGRGKRAGRYGGFLLAAYDEESEELQAICKLGTGFSDEQLEEHYQSLQALVLPT-PRPYVRADGAVAPD
          YLG.GK....YGGFLLAAYDEESEELQAIC.LGTGFS.EQLEEHYQSL.ALVLPT.PRP.VRADGA.APD
Retrocopy YLGQGKWTSHYGGFLLAAYDEESEELQAICNLGTGFSNEQLEEHYQSLEALVLPT<PRPHVRADGALAPD

Parental  HWLDPSAVWEVKCA-DLSLSPIYPAARGLVDSEKGISLRFPRFIRVREDKKPEEATTSAQVACLYRKQSQ
          HWLDP..VWEVKCA..L.LSPIYP.A.GLVDSEKG.SL.FPRFIRV.EDKKPEEATTSA..ACLY.KQSQ
Retrocopy HWLDPNTVWEVKCA<HLCLSPIYPVAQGLVDSEKGLSLHFPRFIRVHEDKKPEEATTSA*AACLYHKQSQ

Parental  IQNQGIDSDSDDEEFY
          IQNQGIDSDSDD.EFY
Retrocopy IQNQGIDSDSDDVEFY

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	0.00 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_914 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_914 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 ,