RetrogeneDB ID: retro_btau_276

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:106967262..106968749(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000004713
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ELP3
• Ensembl ID: ENSBTAG00000002730
• Aliases: None
• Description: Elongator complex protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q2KJ61]

Sequence

>retro_btau_276
ATGAGGCAGAAGCACAAAGGCGATCTCAGCCCTGCTCAGCTAATGATGCTGACCATAGGAGATGTTATTAAACAACTAAT
TGAAGCTCACGAACAGGGAAAAGACATTGATCTAAATAAGGTGAAGACCAGGACAGCTGCCAAATATGGGCTCTTGGCGC
AGCCCCGCCTGGTGGACATCATCGCTGTGGTCCTGCCTCAGTATTGGAAGGTCTTGGTCCCCAAGCTCAAGGCGAAACCC
ATCAGAACTGCCAGTGGGACTGCTGTTGTGGCTGTCATGTGCAAACCCCACAGATGTCCACACATCAGTTTTACAGGAAA
TACATGTGTGTACTGCCCTGGCGGACCTGATTCAGATTTTGAATATTCCACCCAGTCTTACAATGAATATAAGCCAACCT
CCACGTGAGCTATCCATACGAGGTATGACCCTTACCTGCAGACTAGAAACCAGATAGAACAGTTAAAACAACTTGGTCAC
AGGGTGGATAAAGTGGAATTTATCGTGATGGGTGGAACATTTATGGCCCATCCAGAAGAATACAGAGATTATTTTATTCA
AGATTTACATGATGCCTTATCAGGACATACCTCCAACAATATTTATGAGGCCGTCAAGTACTCTGAGAGAAGCCTCACAA
AGTGCATAGGAATTACTATTGAGACCAGACCAGATTACTGCATGAAGTGGCATCTCAGTGACATGTTGACCTACGGCTGC
ATAAGGCTAGAGATTGGGGTGCAGAGTGTCTATGAGGATGTGGCCAGAGATACCAACCGGGGCCACACTGTGAAGGCAGT
GTGCGAGTCCTTCCACCTGGCCAAAGATTCTGGCTTCAAAGTGGTGGCTCACATGATGCCTGATCTGCTGAACGTGGGGC
TGGAGAGAGACACTGAACAGTTTACAGAGTTTTTCAAGAACCCAGCTTTCCATCCTGACGGTTTGAAACTCTACCCTACC
CTGGTGATTCGTGGGACAGGGCTCTATGAGCTCTGGAAGTCAGGAAGATACAAGAGTTATTCCCCCAGCGATCTGATCGA
ATTGGTGGCCCGGATCCTGGCCCTCGTTCCCCCGTGGACTCGAGTGTACCACATGCAGAGAGATATTCCAATGCCGTTAG
TCAGCTCAGGAGTGGAGCACGGAAACTTGAGAGAGCTGGCATTTGCAAGAATGAAAGACCTTGGAATACAGTGTCATGAT
GTGAGAACCAGAGAGGTTGGAATCCAAGAAATTCATCACAAAGTCTGGCCATACCAGGTTGAATTGGTGAGAAGAGATTA
TGTTGCAAATGGAGGCTGGGAAACCTTCTTATCGTACAAAGACCCAGATCAGGACATTTTGATTGGCCTCCTGAGATTAC
AGAAGTGTTCAGAGGAGACATTCCGTTTCGAATTGGTTGGGGGTGTGTCCATAGTCCAAGAGCTGCACGTGTACGGAAGT
GTGGTCCCTGTAAGCAGTCGGGATCCCACTAAATTCAGCATCAGGGC

Alignment

ORF - retro_btau_276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 90.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRQKRKGDLSPAQLMMLTIGDVIKQLIEAHEQGKDIDLNKVKTRTAAKYGLSAQPRLVDIIAAVPPQYRK
          MRQK.KGDLSPAQLMMLTIGDVIKQLIEAHEQGKDIDLNKVKTRTAAKYGL.AQPRLVDIIA.V.PQY.K
Retrocopy MRQKHKGDLSPAQLMMLTIGDVIKQLIEAHEQGKDIDLNKVKTRTAAKYGLLAQPRLVDIIAVVLPQYWK

Parental  VLVPKLKAKPIRTASGIAVVAVMCKPHRCPHISFTGNICVYCPGGPDSDFEYSTQSYTGYEPTSMRAIRA
          VLVPKLKAKPIRTASG.AVVAVMCKPHRCPHISFTGN.CVYCPGGPDSDFEYSTQSY..Y.PTS..AI..
Retrocopy VLVPKLKAKPIRTASGTAVVAVMCKPHRCPHISFTGNTCVYCPGGPDSDFEYSTQSYNEYKPTST*AIHT

Parental  RYDPYLQTRHRIEQLKQLGHSVDKVEFIVMGGTFMALPEEYRDYFIRNLHDALSGHTSNNIYEAVKYSER
          RYDPYLQTR..IEQLKQLGH.VDKVEFIVMGGTFMA.PEEYRDYFI..LHDALSGHTSNNIYEAVKYSER
Retrocopy RYDPYLQTRNQIEQLKQLGHRVDKVEFIVMGGTFMAHPEEYRDYFIQDLHDALSGHTSNNIYEAVKYSER

Parental  SLTKCIGITIETRPDYCMKRHLSDMLTYGCTRLEIGVQSVYEDVARDTNRGHTVKAVCESFHLAKDSGFK
          SLTKCIGITIETRPDYCMK.HLSDMLTYGC.RLEIGVQSVYEDVARDTNRGHTVKAVCESFHLAKDSGFK
Retrocopy SLTKCIGITIETRPDYCMKWHLSDMLTYGCIRLEIGVQSVYEDVARDTNRGHTVKAVCESFHLAKDSGFK

Parental  VVAHMMPDLPNVGLERDIEQFTEFFENPAFRPDGLKLYPTLVIRGTGLYELWKSGRYKSYSPSDLIELVA
          VVAHMMPDL.NVGLERD.EQFTEFF.NPAF.PDGLKLYPTLVIRGTGLYELWKSGRYKSYSPSDLIELVA
Retrocopy VVAHMMPDLLNVGLERDTEQFTEFFKNPAFHPDGLKLYPTLVIRGTGLYELWKSGRYKSYSPSDLIELVA

Parental  RILALVPPWTRVYRVQRDIPMPLVSSGVEHGNLRELAFARMKDLGIQCRDVRTREVGIQEIHHKVRPYQV
          RILALVPPWTRVY..QRDIPMPLVSSGVEHGNLRELAFARMKDLGIQC.DVRTREVGIQEIHHKV.PYQV
Retrocopy RILALVPPWTRVYHMQRDIPMPLVSSGVEHGNLRELAFARMKDLGIQCHDVRTREVGIQEIHHKVWPYQV

Parental  ELVRRDYVANGGWETFLSYEDPDQDILIGLLRLRKCSEETFRFELVGGVSIVRELHVYGSVVPVSSRDPT
          ELVRRDYVANGGWETFLSY.DPDQDILIGLLRL.KCSEETFRFELVGGVSIV.ELHVYGSVVPVSSRDPT
Retrocopy ELVRRDYVANGGWETFLSYKDPDQDILIGLLRLQKCSEETFRFELVGGVSIVQELHVYGSVVPVSSRDPT

Parental  KF-QHQG
          KF.QHQG
Retrocopy KF<QHQG

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	0.07 RPM	8.94 RPM
ERP005899_muscle	0.00 RPM	14.94 RPM
SRP017611_brain	0.09 RPM	31.66 RPM
SRP017611_kidney	0.00 RPM	23.47 RPM
SRP017611_liver	0.15 RPM	17.06 RPM
SRP030211_testis	0.05 RPM	23.69 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_276 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_276 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002730	1 retrocopy	retro_btau_276 ,