RetrogeneDB ID: retro_btau_1692

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:2503605..2506190(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITCH
• Ensembl ID: ENSBTAG00000000308
• Aliases: None
• Description: E3 ubiquitin-protein ligase Itchy homolog [Source:RefSeq peptide;Acc:NP_001075897]

Sequence

>retro_btau_1692
ATGTCTGACAGTGGATCACAGCTTGGTTCAATGGGTAGTTTGACCATGAAATCACAACTTCAGATCACTGTCATTTCAGC
AAAACTTAAAGAAAATAAAAAGAATTGGTTTGGGCCAAGTCCTTATGTGGAAGTCACAGTAGATGGACAGTCAAAGAAGA
CAGAAAAATGCAACAATACGAACAGTCCCAAATGGAAGCAGCCTCTTACAGTTATTGTCACCCCTATGAGTAAATTACAT
TTTCGTGTGTGGAGTCACCAGACACTGAAATCTGATGTTTTGTTGGGAACTGCTGGATTGGATATCTATGAAACATTAAA
GTCAAACAATATGAAACTTGAGGAAGTAGTTGTGACTTTACAGCTTGTAGGTGACAAAGAACCAGCAGAAACAATAGGAG
ATTTGTCAGTCTGTCTTGATGGGCTGCAATTAGAGTCTGAAGTTGTTGCCCATGGTGAAACTGCATGTTCAGAAAGTGCT
TCACAGAATGATGATGGCTCCAGGCCCAAGGATGAAACGAGAGCAAACGCAAGTGGATCAGATGACCCTGAGGATGCAGG
GTCTGGTGAAAACAGGAGGATCAATGGGAATAATTCTCCATCACTCTCAAATGGCGGTTTTAAACCTTCTAGGCCTCCAA
GACCTTCACAACCACCTCCACCTACCCCACGTAGACCAGCATCTGTCAATGGCTCACCATCTACCACTTCTGAAAGTGAT
GGCTCCAGTACAGGCTCTCTGCCACCAACAAATACAAATTCAAGTACATCTGAAGGAGCAACATCTGGATTAATAATTCC
TCTTACTATATCTGGAGGTGCAGGCCCTAGACCATTAAATCCTGTACCTCAAGCTCCCCTCCCACCTTGTTGGGAGCAGA
GAGTGGACCAGCATGGGCGAGTTTACTATGTAGATCATATTGAAAAAAGAACAATGTGGGATAGACCAGAACCTCTACCT
CCTGGCTGGGAGTGGCGGGTTGACAACATGGGACGTATTTATTATGTTGACCATTCACAAGAACAACAACGTGGCAGAGG
CCAACCCTGGAATCAGTCCAGAACTATGAACAATGGCAGCTCCAGCGTAGTCAACTTCATGGAGCTATGCAGCAGTTTAA
CCAGAGGTTCATTTATGGGAATCAAGATTTGTTTGCTACATCACAAAATAAAGAATTTGATCCCCTGGGTCCCCTGCCGC
CTGGATGGGAGAAGAGAACGGACAGCAATGGTAGAGTATATTTTGTCAACCACAACACTCGTATTACACAATGGGAAGAC
CCCAGAAATCAAGGTCAATTAAATGAAAAGCCCTTACCTGAAGGCTGGGAAATGAGATTCACGGTAGACGGAATTCCATA
TTTTGTGGACCACAATAGAAGAACAACCACCTATATAGATCCCCGCACGGGAAAATCTGCCTTAGAAAATGGACCCCAGA
TAGCCTATGTACGGGACTTCAAGGCAAAGGTTCAATATTTCCGTTTCTGGTGTCAGCAACTGGCCATGCCACAGCACATA
AAGATTACAGTGACAAGAAAAACGTTGTTTGAGGATTCCTTTCAGCAGATAATGAGCTTCAGTCCTCAAGATCTGTGAAG
ACGTTTGTGGGTGATTTTTCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAGAGAATGGTTCTTTCTTTTGTCAC
ATGAGGTGTTGAACCCAATGTATTGCCTGTTTGAATATGCAGGGAAGGATAACTACTGCTTGCAGATAAACCCCGCTTCT
TACATCAATCCAGATCACCTGAAATATTTTCGTTTTATTTGCAGGTTTATTGCTATGGCTCTGTTCCATGGGAAATTCAT
AGACACAGGTTTTTCTTTGCCATTCTATAAGCGTATCTTGAATAAACCAGTTGGACTGAAGGATTTAGAATCGATTGATC
CAGAATTTTACAATTCTCTCATCTGGGTTAAAGAAAACAATATTGAGGAGTGTGATTTGGAAATGTATTTCTCCATTGAT
AAAGAAATCTTAGGTGAAATCAAGAGTCATGATTTGAAACCCAATGGTGGCAATATTCTTGTAACAGAAGAAAATAAAGA
AGAATATATCAGAATAGTAGCTGAATGGAGATTCTCTCGTGGTGTTGAAGAACAGACGCAAGCTTTCTTTGAGGGCTTTA
ATGAAATTCTTCCCCAGCAGTATCTACAGTACTTTGATGCAAAGGAATTAGAGGTTCTTTTATGTGGGATACAAGAGATT
GATTTGAATGATAGGCAAAGACATGCCATCTACCATCACTATACCAGGACAAGTAAACAAATCATGTGGTTTTGGCAGTT
TGTTAAAGAAATCGATAATGAGAAGAGAATGCGACTTTTGCAGTTTGTTACTGGGACCTGCCGACTGTCAGTTGGAGGAT
TTGCTGACCTCATGGGGAGCAATGGGCCACAGAAGTTCTGCATTGAAAAAGTCGGGAAAGAAAATTGGTTGCCTAGACGT
CATACCTGTTTTAACCGCGTGGACCTGCCACCCTACAAGAGCTATGAGCAACTGAAGGAAAAGCTGTTATTTGTTATTGA
AGAAACAGAAGGCTTTGGACAAGAG

Alignment

ORF - retro_btau_1692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDSGSQLGSMGSLTMKSQLQITVISAKLKENKKNWFGPSPYVEVTVDGQSKKTEKCNNTNSPKWKQPLT
          MSDSGSQLGSMGSLTMKSQLQITVISAKLKENKKNWFGPSPYVEVTVDGQSKKTEKCNNTNSPKWKQPLT
Retrocopy MSDSGSQLGSMGSLTMKSQLQITVISAKLKENKKNWFGPSPYVEVTVDGQSKKTEKCNNTNSPKWKQPLT

Parental  VIVTPVSKLHFRVWSHQTLKSDVLLGTAGLDIYETLKSNNMKLEEVVVTLQLVGDKEPAETIGDLSVCLD
          VIVTP.SKLHFRVWSHQTLKSDVLLGTAGLDIYETLKSNNMKLEEVVVTLQLVGDKEPAETIGDLSVCLD
Retrocopy VIVTPMSKLHFRVWSHQTLKSDVLLGTAGLDIYETLKSNNMKLEEVVVTLQLVGDKEPAETIGDLSVCLD

Parental  GLQLESEVVANGETACSESASHNDDGSRPKDETRANASGSDDPEDAGSGENRRINGNNSPSLSNGGFKPS
          GLQLESEVVA.GETACSESAS.NDDGSRPKDETRANASGSDDPEDAGSGENRRINGNNSPSLSNGGFKPS
Retrocopy GLQLESEVVAHGETACSESASQNDDGSRPKDETRANASGSDDPEDAGSGENRRINGNNSPSLSNGGFKPS

Parental  RPPRPSRPPPPTPRRPASVNGSPSTTSESDGSSTGSLPPTNTNSSTSEGATSGLIIPLTISGGAGPRPLN
          RPPRPS.PPPPTPRRPASVNGSPSTTSESDGSSTGSLPPTNTNSSTSEGATSGLIIPLTISGGAGPRPLN
Retrocopy RPPRPSQPPPPTPRRPASVNGSPSTTSESDGSSTGSLPPTNTNSSTSEGATSGLIIPLTISGGAGPRPLN

Parental  PIPQAPLPPGWEQRVDQHGRVYYVDHIEKRTTWDRPEPLPPGWERRVDNMGRIYYVDH-FTRTTTWQRPT
          P.PQAPLPP.WEQRVDQHGRVYYVDHIEKRT.WDRPEPLPPGWE.RVDNMGRIYYVDH.FTRTTTWQRPT
Retrocopy PVPQAPLPPCWEQRVDQHGRVYYVDHIEKRTMWDRPEPLPPGWEWRVDNMGRIYYVDH<FTRTTTWQRPT

Parental  LESVRNYEQWQLQRSQLQGAMQQFNQRFIYGNQDLFATSQNKEFDPLGPLPPGWEKRTDSNGRVYFVNHN
          LESV.NYEQWQLQRSQL.GAMQQFNQRFIYGNQDLFATSQNKEFDPLGPLPPGWEKRTDSNGRVYFVNHN
Retrocopy LESVQNYEQWQLQRSQLHGAMQQFNQRFIYGNQDLFATSQNKEFDPLGPLPPGWEKRTDSNGRVYFVNHN

Parental  TRITQWEDPRNQGQLNEKPLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALDNGPQIAYVRDFKA
          TRITQWEDPRNQGQLNEKPLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSAL.NGPQIAYVRDFKA
Retrocopy TRITQWEDPRNQGQLNEKPLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALENGPQIAYVRDFKA

Parental  KVQYFRFWCQQLAMPQHIKITVTRKTLFEDSFQQIMSFSPQDLRRRLWVIFPGEEGLDYGGVAREWFFLL
          KVQYFRFWCQQLAMPQHIKITVTRKTLFEDSFQQIMSFSPQDL.RRLWVIFPGEEGLDYGGVAREWFFLL
Retrocopy KVQYFRFWCQQLAMPQHIKITVTRKTLFEDSFQQIMSFSPQDL*RRLWVIFPGEEGLDYGGVAREWFFLL

Parental  SHEVLNPMYCLFEYAGKDNYCLQINPASYINPDHLKYFRFIGRFIAMALFHGKFIDTGFSLPFYKRILNK
          SHEVLNPMYCLFEYAGKDNYCLQINPASYINPDHLKYFRFI.RFIAMALFHGKFIDTGFSLPFYKRILNK
Retrocopy SHEVLNPMYCLFEYAGKDNYCLQINPASYINPDHLKYFRFICRFIAMALFHGKFIDTGFSLPFYKRILNK

Parental  PVGLKDLESIDPEFYNSLIWVKENNIEECGLEMYFSVDKEILGEIKSHDLKPNGGNILVTEENKEEYIRM
          PVGLKDLESIDPEFYNSLIWVKENNIEEC.LEMYFS.DKEILGEIKSHDLKPNGGNILVTEENKEEYIR.
Retrocopy PVGLKDLESIDPEFYNSLIWVKENNIEECDLEMYFSIDKEILGEIKSHDLKPNGGNILVTEENKEEYIRI

Parental  VAEWRLSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGMQEIDLNDWQRHAIYRHYTRTSKQIM
          VAEWR.SRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCG.QEIDLND.QRHAIY.HYTRTSKQIM
Retrocopy VAEWRFSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGIQEIDLNDRQRHAIYHHYTRTSKQIM

Parental  WFWQFVKEIDNEKRMRLLQFVTGTCRLPVGGFADLMGSNGPQKFCIEKVGKENWLPRSHTCFNRLDLPPY
          WFWQFVKEIDNEKRMRLLQFVTGTCRL.VGGFADLMGSNGPQKFCIEKVGKENWLPR.HTCFNR.DLPPY
Retrocopy WFWQFVKEIDNEKRMRLLQFVTGTCRLSVGGFADLMGSNGPQKFCIEKVGKENWLPRRHTCFNRVDLPPY

Parental  KSYEQLKEKLLFAIEETEGFGQE
          KSYEQLKEKLLF.IEETEGFGQE
Retrocopy KSYEQLKEKLLFVIEETEGFGQE

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	0.00 RPM	67.34 RPM
ERP005899_muscle	0.11 RPM	51.63 RPM
SRP017611_brain	0.37 RPM	99.44 RPM
SRP017611_kidney	0.47 RPM	121.86 RPM
SRP017611_liver	0.30 RPM	45.61 RPM
SRP030211_testis	0.64 RPM	90.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1692 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1692 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	ENSBTAG00000000308	1 retrocopy	retro_btau_1692 ,
Choloepus hoffmanni	ENSCHOG00000011115	1 retrocopy	retro_chof_2100,
Felis catus	ENSFCAG00000008780	1 retrocopy	retro_fcat_899,