RetrogeneDB ID: retro_btau_1810

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:41634345..41636735(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS35
• Ensembl ID: ENSBTAG00000002493
• Aliases: None
• Description: Vacuolar protein sorting-associated protein 35 [Source:UniProtKB/Swiss-Prot;Acc:Q2HJG5]

Sequence

>retro_btau_1810
ATGCCTACAACACAGCAGTCACCGCAGGATGAGCAGGAAAAACTCTTTGATTAAGCCATACAGGCTGTGAAGGTCCAGTC
ATTCCAGATGAAGAGATGCCTGGACAAAAACAAGCTTATGGATGCTCTGAAACATGCTTCTAATATGCTTGGTGAACTGT
GGACTTCCATGTTATCACCAAAAAGCTACTATGAACTTTATATGGATATTTCTGATGAACTGCACTACTTGGAAGTTTAC
CTGACAGATGAATTTGCTAAAGGAAGAAAAGTGGCAGATCTCTATGAACTTGTACAGTATGCCGGAAACATTATCCCAAG
GCTTTATCTGTTGATCACAGTTGGAGTTGTATACGTCAAGTCATTTCCTCAGTCCAGGAAAGATATTTTGAAAGATTTGG
TAGAAATGTGCCGTGGTGTGCAACATCCCTTGAGAGGTCTATTTCTTCGAAATTATCTACTTCAGTGTACCAGAAACATC
TTACCTGATGAAGGGGAGCCAACAGATGAAGAAACAACTGGTGATATCAGTGATTCCATGGATTTTGTCCTACTCAACTT
TGCAGAAATGAACAAGCTCTGGGTTCGAATGCAGCATCAGGGACATAGCCAAGATAGATAAAAAAGAGAACAAGAAAGAC
AAGAACTGAGAATTTTAGTGGGAACAAATTTGGTGCGCCTTAGTCAGTTGGAAGGTCTAAATGTGGAACGTTACAAACAG
ATTGTTTTGACCAGCATATTGGAGCAAGTGGTGAATTGCAGAGATGCTTTGGCTCAGGAATATCTCATGGAATGCATTAT
TCAGGTTTTCCCTGATGAATTCCACCTTCAAACTTTGAATCCTTTTCTTCGGGCCTGTGCTGAGTTACACCAAAATGTAA
ATATGAAAAACATAATCATTGCTTTAATTGATAGATTAGCTTTATTTGCTCACCGTGAAGATGGACCTGGAATCCCAACA
GATATTAAACTTTTTGACATATTTTCACAGCAGGTGGCTACAGTAATACAGTCTAGACAAGACATGCTTTCGGAAGATGT
TGTATCTTTACAAGTCTCTCTCATTAATCTCACTATGAAGTGTTATCCTGACCGTGTGGACTATGTTGATAAAGTTCTAG
AAACAACAGTGGAGATATTTAATAAGCTCAACCTTGAACATATTGCTACCAGTAGTGCAGTTTCAAAGGAGCTCACCAGA
CTTTTGAAGATTCCTGTTGACACTTACAACAATATTTTAACAGTCTTGAAATTAAAACATTTCCACCCACTCTTTGAGTA
TTTTGACTATGAGTCCAGAAAGAGCATGAGTTGTTACGTGCTTAGTAATGTTCTAGATTATAATACAGAAATTGTCTCTC
AAGACCAGGAGGATTCCATAATGAATTTGGTATCTACACTGACTGAGGATTAGCCAGATCAACCTGTAGAAGAACCTGAG
CCAGAGGACTTTGCTGATGAGCAGAGCCTTGTGGGCGGATTCATTCATCTTCTACGGTCTGAGGACCCTGATCAACAGTA
CTTGATTTTAAATACAGCACGAAAATATTTTGGAGCTGGTGGAAATCAACAGATTTGCTCCACACTGCCACCTTTGGTAT
TTGCAGCTTACCAGCTGGCTTTTCGCTACAAAGAGAATTCTAAAGTGGATGACAAATGGGAAAAGAAATGCTAGAAGATT
TTTTCATTTACTCACCAGACTATTAGTGCTTTGATCAAAGCAGAGCTGGCAGAATTACCCTTAAGACTTTTTCTTCAGAG
GGCTCTAGCTGCTGGAGAAATTGGTTTTGAAAATCATGAAACAGTAGCATATGAATTTATGTCCCAGGCATTTTCTCTGT
ATGAAGATGAAATCAGTGATTTCAAAGCACAACTGGCTGCCATCACCTTGATCATTGGTACTTTTGAGAGGATGAAGTGC
TTCAGTGAAGAAAACCATGAACCCTTGAGGATTCAGTGTGCTCTTGCTGCATCCAAACTTCTGAAGAAGCCTGATCAGGG
CCGAGCTGTGAGCACCTGTGCACATTTCTTTTGGTCTGGCAGAAACACAGACAAAAATGGAGAGGAGCTGCATGGAGGCA
AAAGGGTAATGGAATGCTAAAGAAAGCTCTGAAAATAGCAAATCAGTGCATGGACCCCTCTCTATAAAAAGTGCAACTTT
TTATAGAAATCCTGAACAGATGTATATATTTTTATGAAAAGGAAAATGATGTGGTCACTATTCAGGTTTTGAATCAGCTT
ATCCAAAAGATTCGAGAAGACCTCCCAAATCTTGAATCCAGTGAAGAAACAGAGCAGATTAACAAACATTTTCATAACAC
AATGGAGCACTTGTGCTTAAGGCGGGAAACACCAGAATCTGAAGGGCCAATTTATGAGGGTCTCATCCTT

Alignment

ORF - retro_btau_1810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPTTQQSPQDEQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAI
          MPTTQQSPQDEQEKL.D.AIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGEL.TSMLSPKSYYELYM.I
Retrocopy MPTTQQSPQDEQEKLFD*AIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELWTSMLSPKSYYELYMDI

Parental  SDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGV
          SDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGV
Retrocopy SDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGV

Parental  QHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRE
          QHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHS.DR.KRE
Retrocopy QHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSQDR*KRE

Parental  RERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLN
          .ERQELRILVGTNLVRLSQLEG.NVERYKQIVLT.ILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLN
Retrocopy QERQELRILVGTNLVRLSQLEGLNVERYKQIVLTSILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLN

Parental  PFLRACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPTDIKLFDIFSQQVATVIQSRQDMPSEDVVSL
          PFLRACAELHQNVN.KNIIIALIDRLALFAHREDGPGIPTDIKLFDIFSQQVATVIQSRQDM.SEDVVSL
Retrocopy PFLRACAELHQNVNMKNIIIALIDRLALFAHREDGPGIPTDIKLFDIFSQQVATVIQSRQDMLSEDVVSL

Parental  QVSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKH
          QVSLINL.MKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKH
Retrocopy QVSLINLTMKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKH

Parental  FHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQPVEEPDPEDFADEQSL
          FHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQ.DSIMNLVSTL..D.PDQPVEEP.PEDFADEQSL
Retrocopy FHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQEDSIMNLVSTLTED*PDQPVEEPEPEDFADEQSL

Parental  VGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAFRYKENSKVDDKWEKKCQKI
          VG.FIHLLRSEDPDQQYLILNTARK.FGAGGNQ.I..TLPPLVFAAYQLAFRYKENSKVDDKWEKKC.KI
Retrocopy VGGFIHLLRSEDPDQQYLILNTARKYFGAGGNQQICSTLPPLVFAAYQLAFRYKENSKVDDKWEKKC*KI

Parental  FSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITL
          FSF.HQTISALIKAELAELPLRLFLQ.ALAAGEIGFENHETVAYEFMSQAFSLYEDEISD.KAQLAAITL
Retrocopy FSFTHQTISALIKAELAELPLRLFLQRALAAGEIGFENHETVAYEFMSQAFSLYEDEISDFKAQLAAITL

Parental  IIGTFERMKCFSEENHEPLRTQCALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMEC-
          IIGTFERMKCFSEENHEPLR.QCALAASKLLKKPDQGRAVSTCAH.FWSGRNTDKNGEELHGGKRVMEC.
Retrocopy IIGTFERMKCFSEENHEPLRIQCALAASKLLKKPDQGRAVSTCAHFFWSGRNTDKNGEELHGGKRVMEC<

Parental  LKKALKIANQCMDPSL-QVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINK
          LKKALKIANQCMDPSL..VQLFIEILNR.IYFYEKEND.VTIQVLNQLIQKIREDLPNLESSEETEQINK
Retrocopy LKKALKIANQCMDPSL*KVQLFIEILNRCIYFYEKENDVVTIQVLNQLIQKIREDLPNLESSEETEQINK

Parental  HFHNTLEHLRLRRESPESEGPIYEGLIL
          HFHNT.EHL.LRRE.PESEGPIYEGLIL
Retrocopy HFHNTMEHLCLRRETPESEGPIYEGLIL

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
ERP005899_liver	0.22 RPM	63.88 RPM
ERP005899_muscle	0.26 RPM	82.67 RPM
SRP017611_brain	0.46 RPM	87.29 RPM
SRP017611_kidney	0.24 RPM	98.15 RPM
SRP017611_liver	0.08 RPM	26.73 RPM
SRP030211_testis	0.16 RPM	73.29 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1810 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1810 has 0 orthologous retrocopies within eutheria group .

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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,