RetrogeneDB ID: retro_btau_1002

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:9782078..9782889(+)
• Located in intron of: ENSBTAG00000016838

Retrocopy information

• Ensembl ID: ENSBTAG00000046180
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.86811
• Ensembl ID: ENSBTAG00000009378
• Aliases: None
• Description: None

Sequence

>retro_btau_1002
AAGGCGGCTGCAGATTACTTTGGCTGTGAGGCAAAAAAGAAGAATTTATGATATCACCAATGTCTTGGAAGGAATTGACT
TAATTGAAAAAAAGTCAAAAAACAGTATACAATGGAAAGGGGTAGGTGCTGGCTGTAATACTAAAGAAGTCATAGATAGA
TTAAAATATCTCAAAGCTGAAATTGAAGATCTAGAACTGAAGGAAAGAGAACTTGATCAGCAGAAGTTGTGGCTACAGCA
AAGCATCAAAAATGTGATGGACGACTCCATTAATAATAGATTTTCCTATGTAACTCATGAAGACATCTGTAATTGTTTTA
ATGGTGATACACTTTTGGCCATTCAAGCACCTTCTGGTACACAACTGGAGGTACCTATTCCAGAAATGGGTCAGAATGGA
CAAAAGAAATACCAGATCAATCTAAAGAGTCATTCAGGACCTATCCACGTGCTGCTTATAAATAAAGAGTCCAGCTCATC
TAAGCCCGTGGTTTTTCCGGTGCCCCCCTCAGACGACCTCGCGCAGCCTCCCTCTCAGCCTCCTACCCCAGTGCCTCCAC
ACAAGCCCAGCTCGGCCGTCCAGAGCCTGCCTGAGCCACCTGTCTCTGAACGAAGCCAGCCTCTCCAGCACACGCCAGCC
ACCGACTTGTCTTCAGCAGGATCTATTAGTGGAGATATCATTGATGAGTTAATGTCTTCTGATGTGTTTCCGCTCTTACG
GCTTTCTCCGACCCCAGCAGATGACTACAACTTTAATTTAGATGATAATGAAGGCGTTTGTGATCTGTTTGATGTTCAGA
TACTAAATTAT

Alignment

ORF - retro_btau_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQAAD-TLAVRQKRRIYDITNVLEGIDLIEKKSKNSIQWKGVGAGCNTKEVIDRLKYLKAEIEDLELKER
          K.AAD.TLAVRQKRRIYDITNVLEGIDLI......SIQWKGVGAGCNTKEVIDRLKYLKAEIEDLELKER
Retrocopy KAAAD>TLAVRQKRRIYDITNVLEGIDLIXXXXXXSIQWKGVGAGCNTKEVIDRLKYLKAEIEDLELKER

Parental  ELDQQKLWLQQSIKNVMDDSINNSTFSYVTHEDICNCFNGDTLLAIQAPSGTQLEVPIPEMGQNGQKKYQ
          ELDQQKLWLQQSIKNVMDDSINN..FSYVTHEDICNCFNGDTLLAIQAPSGTQLEVPIPEMGQNGQKKYQ
Retrocopy ELDQQKLWLQQSIKNVMDDSINNR-FSYVTHEDICNCFNGDTLLAIQAPSGTQLEVPIPEMGQNGQKKYQ

Parental  INLKSHSGPIHVLLINKESSSSKPVVFPVPPPDDLAQPPSQPPTPVPPHKPSSAVQSLPEPPVSERSQPL
          INLKSHSGPIHVLLINKESSSSKPVVFPVPP.DDLAQPPSQPPTPVPPHKPSSAVQSLPEPPVSERSQPL
Retrocopy INLKSHSGPIHVLLINKESSSSKPVVFPVPPSDDLAQPPSQPPTPVPPHKPSSAVQSLPEPPVSERSQPL

Parental  QHTPATDLSSAGSISGDIIDELMSSDVFPLLRLSPTPADDYNFNLDDNEGVCDLFDVQILNY
          QHTPATDLSSAGSISGDIIDELMSSDVFPLLRLSPTPADDYNFNLDDNEGVCDLFDVQILNY
Retrocopy QHTPATDLSSAGSISGDIIDELMSSDVFPLLRLSPTPADDYNFNLDDNEGVCDLFDVQILNY

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	7.35 RPM
ERP005899_muscle	0.84 RPM	4.43 RPM
SRP017611_brain	0.50 RPM	8.63 RPM
SRP017611_kidney	1.42 RPM	8.12 RPM
SRP017611_liver	0.45 RPM	4.23 RPM
SRP030211_testis	3.09 RPM	17.54 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1002 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1002 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	ENSBTAG00000009378	1 retrocopy	retro_btau_1002 ,
Bos taurus	ENSBTAG00000021045	1 retrocopy	retro_btau_1523,
Bos taurus	ENSBTAG00000048286	1 retrocopy	retro_btau_1820,
Monodelphis domestica	ENSMODG00000005958	1 retrocopy	retro_mdom_1064,