RetrogeneDB ID: retro_cpor_880

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_31:5444311..5445803(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS35
• Ensembl ID: ENSCPOG00000003773
• Aliases: None
• Description: None

Sequence

>retro_cpor_880
ATCATTGCTTTAATTGATAGATTAGCTTTATTTTCTCATCGTGAAGATGGACCTGGGATTCCAGCAGATATTAAACTTTT
TGATATATTTTCACAGCAGGTGGCCACAGTGATACAATCTAGACAAGACATGCCTTCCGAGGATGTTGTATCTTTACAAG
TGTCTCTCATTAATCTTGCCATGAAATGTTACCCTGATCATGTGGACTATGTGGATAAAGTTCTGGAAACAATGGTGGAG
ATATTCAACAAGCTCAACCTTGAACATATTGCTACCAGTAGTGCAGTTTCAAAGGAACTCACCAGACTTTTGAAGATACC
TGTTGATACTTACAACAATATTTTGACCGTCTTGAAATTGAAACATTTCCACCCACTGTTTGAGTACTTTGACTATGAGT
CCAGAAAGAGTATGAGTTATTATGTGCTTAGTAATGTTCTGGATTATAATACAGAAATTGTCTCTCAAGACCAGGTGGAT
TCCATAATGAATTTGGTGTCCACATTGATTCAAGATCAGCCAGATCAACCTATGGAAGACCCCTGATCCAGAAGACTTTG
CAGATGAGCAGAGCCTTGTGGGCTGATTCATTCATCTTCTTCGGTCTGAGGACCCTAATCAGCAGTACTTGATCTTAAAT
ACAGCATGAAAGCATTTTGGAGCTGGTGGAAATCAGCGGATTCGCTTCACACTGCCACCTTTGGTGTTTGCTGCTTACCA
GCTGGCTTTTCGATACAAAGAGAATTCTAAAGTGGATAACAAATGGGAAAAAAAATGCCAGATCTTTTCATTTGCTCACC
AGACTATTGGTGCTTTGATCAAAGCAGAGCTGGCAGAATTACCCTTAAGACTTTTTCTTCAGGGAGCCCTAGCTGCTGGT
GAGATTGGCTTTGAAAATCATGAAACAGTAGCATATGAATTTATGTCCCAGGCATTTTCCCTGTATGAAGATGAAATCAG
TGATTCCAAAGCACAGCTGGCTGCCATCACATTGATTATTGGTACTTTTGAAAGGATGAAATGCTTCAGTGAAGAGAATC
ATGAACCCTTGAGAACTCAGTGTGCACTTGCTGCATCCAAACTTCTAAAAAAGCCCGATCAGGGCTGAGCCATGAGCACC
TGTGCACATCTCTTCTGGTCCGGCAGAAACACAGACAAAAATGGAGAGGAGCTTCATGGAGGGAAGAGGGTCATAGAGTG
CCTAAAGAAAGCTCTAAAAATAGCAAATCAGTGCATGGACCCCTCTCTACAAGTGCAACTTTTTATAGAAATTCTGAACA
GATATATCTATTTTTATGAAAAGGAAAATGATGCGGTAACAATTCAGGTGTTGAATCAGTTTATCCAAAAGATTCGAGAA
GACCTCCCAAACCTTGAGTCCGGTGAAGAAACAGAACAGAGTAACAAACATTTTCATAACACACTAGAGCATTTGCGTTT
GAGGCGGGAATCACCAGAGTCTGAGGGTCCAATTTATGAAGGTCTTGTCCTT

Alignment

ORF - retro_cpor_880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.79 %
• Parental protein coverage: 62.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IIALIDRLALFAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLIKLAMKCYPDRVDY
          IIALIDRLALF.HREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLI.LAMKCYPD.VDY
Retrocopy IIALIDRLALFSHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDHVDY

Parental  VDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDYESRKSMSC
          VDKVLET.VEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDYESRKSMS.
Retrocopy VDKVLETMVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDYESRKSMSY

Parental  YVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQPVEDP-DPEDFADEQSLVGRFIHLLRSEDPDQQY
          YVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQP.EDP.DPEDFADEQSLVG.FIHLLRSEDP.QQY
Retrocopy YVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQPMEDP>DPEDFADEQSLVG*FIHLLRSEDPNQQY

Parental  LILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAFRYKENSKVDDKWEKKCQKIFSFAHQTISALIKAELA
          LILNTA.KHFGAGGNQRIRFTLPPLVFAAYQLAFRYKENSKVD.KW...CQ.IFSFAHQTI.ALIKAELA
Retrocopy LILNTA*KHFGAGGNQRIRFTLPPLVFAAYQLAFRYKENSKVDNKWXXXCQ-IFSFAHQTIGALIKAELA

Parental  ELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHE
          ELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHE
Retrocopy ELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHE

Parental  PLRTQCALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQV
          PLRTQCALAASKLLKKPDQG.A.STCAHLFWSGRNTDKNGEELHGGKRV.ECLKKALKIANQCMDPSLQV
Retrocopy PLRTQCALAASKLLKKPDQG*AMSTCAHLFWSGRNTDKNGEELHGGKRVIECLKKALKIANQCMDPSLQV

Parental  QLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESGEETEQINKHFHNTLEHLRLRRESPESE
          QLFIEILNRYIYFYEKENDAVTIQVLNQ.IQKIREDLPNLESGEETEQ.NKHFHNTLEHLRLRRESPESE
Retrocopy QLFIEILNRYIYFYEKENDAVTIQVLNQFIQKIREDLPNLESGEETEQSNKHFHNTLEHLRLRRESPESE

Parental  GPIYEGLVL
          GPIYEGLVL
Retrocopy GPIYEGLVL

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	1.50 RPM	82.65 RPM
SRP017611_kidney	1.99 RPM	75.48 RPM
SRP017611_liver	1.18 RPM	43.27 RPM
SRP040447_lung	0.18 RPM	81.41 RPM
SRP040447_skeletal_muscle	0.08 RPM	26.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_880 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_880 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002493	1 retrocopy	retro_btau_1810,
Callithrix jacchus	ENSCJAG00000010203	1 retrocopy	retro_cjac_2066,
Cavia porcellus	ENSCPOG00000003773	1 retrocopy	retro_cpor_880 ,