RetrogeneDB ID: retro_btau_1192

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:20297259..20298062(-)
• Located in intron of: ENSBTAG00000001043

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPAF1
• Ensembl ID: ENSBTAG00000000094
• Aliases: None
• Description: None

Sequence

>retro_btau_1192
AGTGGGAACGGCCGTGGCTCCTGCGGTGATAGGGGGCCCGGCCTCTAGGGCGGCCTGTGCGCAGTTCGCAGCCCCGCCCT
GGGCCTGGGGCTCCTGTCGCCTCGCAGTGATCCCGGTGCGCGCCGCAGCTCCAGCTGGCCCGCCAGGGGCGCCATTGGTA
GCGGGGGTCAGAAAGGCGCTCGAAGCCAACCCCTTCTAGGACCGCTACTGCAAAAAGATCCAGCAGTTGTGCAGGTCTGA
CTCAGCTGCTTTTGAGTCCTGACTAGAGAAGTGCAGTGAGTTTAGCAAGCAGCCAGTGGGGCACTCCAAGCAAGGGGACT
TTATCCCATGTGTGGCACGGAAGACACTGGGGAAACGGCCTGTGAGCCGAGGATTCACTAAGGACTAGACTCTCAGTTCA
ATCTTCAACATTGAGATGGTGAAAGACAAAACTGCCGAAGAAATAAAACAGATTTGGCAGCAGTATTTTGCAGCAAAAGA
GAACAGTCTACGCAGTTATTCCTAAAAAGTTTGATTTGATTTGGAACCGGGCTTAGTCCTGTCCAACATTTCTGTGTGGC
CTACCAAGAAGGGAAGGTTATGAGTTTTTTGTCCGGCAATGGACAGGTACTGAACTCCACTTCACTGCACTTATAAATAT
TCAGATCCCAGGGGAAGCTGCGGCCAGTCAGCTGATTCTATATCATTACCCTGAACTTAAGGAAGAAAATAGTATAGTGC
TAATGACAGCAGAAATGGATTCCACATTTCTGAATGATGCTGAGGCACAGTGCCTGGCCAACAAAGTTCAGCTCTTCTAT
GCA

Alignment

ORF - retro_btau_1192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.1 %
• Parental protein coverage: 83.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAGGAGPAVLQVAGLYRGLCAVRSRALGLGLVSAAQLRVFPVRRSSGRPAGGADGSA-VGDELEANPFYD
          ...G.G.......GL..GLCAVRS.A..LGL...........RRSS..PA.GA.GS..V...LEANPF.D
Retrocopy SGNGRGSCGDRGPGL*GGLCAVRSPA--LGLGLLSPRSDPGARRSSSWPARGAIGSG>VRKALEANPF*D

Parental  RYRDKIQQLRRSDPAAFESRLEKRSEFRKQPVGHSRQGDFIKCVEQKTLGKQPVSRGFTKDKTLSSIFNI
          RY..KIQQL.RSD.AAFES.LEK.SEF.KQPVGHS.QGDFI.CV..KTLGK.PVSRGFTKD.TLSSIFNI
Retrocopy RYCKKIQQLCRSDSAAFES*LEKCSEFSKQPVGHSKQGDFIPCVARKTLGKRPVSRGFTKD*TLSSIFNI

Parental  EMVKGKTAEEIKQIWQQYFAAKD-TVYAVIPKEKFDLIWNRAQSCPTFLCALPRREGYEFFVGQWTGTEL
          EMVK.KTAEEIKQIWQQYFAAK..TVYAVIPK.KFDLIWNRA.SCPTFLC.LPRREGYEFFV.QWTGTEL
Retrocopy EMVKDKTAEEIKQIWQQYFAAKE>TVYAVIPK-KFDLIWNRA*SCPTFLCGLPRREGYEFFVRQWTGTEL

Parental  HFTALINIQTRGEAAASQLILYHYPELKEEKGIVLMTAEMDSTFLSVAEAQCMANQVQLFYA
          HFTALINIQ..GEAAASQLILYHYPELKEE..IVLMTAEMDSTFL..AEAQC.AN.VQLFYA
Retrocopy HFTALINIQIPGEAAASQLILYHYPELKEENSIVLMTAEMDSTFLNDAEAQCLANKVQLFYA

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	22.49 RPM
ERP005899_muscle	0.00 RPM	15.78 RPM
SRP017611_brain	0.00 RPM	20.42 RPM
SRP017611_kidney	0.00 RPM	34.44 RPM
SRP017611_liver	0.00 RPM	23.86 RPM
SRP030211_testis	0.04 RPM	50.80 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1192 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1192 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000094	1 retrocopy	retro_btau_1192 ,
Cavia porcellus	ENSCPOG00000003349	1 retrocopy	retro_cpor_965,
Mustela putorius furo	ENSMPUG00000012737	1 retrocopy	retro_mputfur_1060,
Mus musculus	ENSMUSG00000028710	1 retrocopy	retro_mmus_1982,