RetrogeneDB ID: retro_btau_1389

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:70910365..70911247(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000001858
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSBTAG00000012975
• Aliases: None
• Description: Voltage-dependent anion-selective channel protein 2 [Source:UniProtKB/Swiss-Prot;Acc:P68002]

Sequence

>retro_btau_1389
ATGGCGACCTATGGACAGAACTGCACGCGGCCAGTGTGTATTCCTCCATCATATGCTGACCTTGGCAAAGCTGCCAGAGA
TATATTCAACAAAGGATTTGGTTTTGGGTTGGTGAAACTGGATGTGAAAACAAAGTCGTGCAGTGGCGTGGAATTCTCAA
CATCTGGTTCATCTAATACAGACACTGGTAAAGTTACTGGGACCTTGGAGACCAAATATAAATGGTGTGAGTATGGTCTG
ACTTTCACAGAAAAGTGGAACACTGATAACACTCTGGGAACAGAAATCGCTATTAAAGACCAGATTTGCCAAGGTTTGAA
ACTGACATTTGATACCACCTTTTCACCAAACACAGGAAAGAAAAGTGGTAAAATCAAGTCTTCTTACAAGAGGGAATGTA
TAAACCTTGGTTGTGATGTTGACTTTGATTTTGCTGGACCTGCAATCCATGGTTCGGCTGTCTTCGGTTATAAGGGCTGG
CTTGCTGGGTACCAGATGACCTTTGACAGTGCCAAATCAAAGCTGACAAGGAATAACTTTGCAGTGGGCTACAGGACTGG
GGACTTCCAGCTACACACTAATGTCAATGATGGTACAGAATTTGGAGGATCAATTTATCAGAAAGTATGTGAAGATCTTG
ACACTTCAGTAAACCTTGCTTGGACATCAGGAACCAACTGCACTCGCTTTGGAATTGCAGCTAAATATCAACTGGATCCC
ACTGCTTCCATTTCTGCAAAAGTCAACAACTCTAGTTTAATTGGAGTGGGCGATACTCAGACTCTGAGGCCTGGTGTGAA
GCTTACACTGTCTGCCCTGGTAGACGGGAAGAACATTAATGCTGGAGGCCACAAACTTGGGCTTGCCCTGGAATTGGAGG
CT

Alignment

ORF - retro_btau_1389 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATYGQNCARPMCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLE
          MATYGQNC.RP.CIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLE
Retrocopy MATYGQNCTRPVCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLE

Parental  TKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDV
          TKYKWCEYGLTFTEKWNTDNTLGTEIAI.DQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDV
Retrocopy TKYKWCEYGLTFTEKWNTDNTLGTEIAIKDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDV

Parental  DFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVC
          DFDFAGPAIHGSAVFGY.GWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVC
Retrocopy DFDFAGPAIHGSAVFGYKGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVC

Parental  EDLDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSIN
          EDLDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVG.TQTLRPGVKLTLSALVDGK.IN
Retrocopy EDLDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGDTQTLRPGVKLTLSALVDGKNIN

Parental  AGGHKLGLALELEA
          AGGHKLGLALELEA
Retrocopy AGGHKLGLALELEA

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	2.67 RPM	53.64 RPM
ERP005899_muscle	10.87 RPM	144.01 RPM
SRP017611_brain	6.58 RPM	75.46 RPM
SRP017611_kidney	15.88 RPM	176.04 RPM
SRP017611_liver	2.04 RPM	26.05 RPM
SRP030211_testis	17.26 RPM	210.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1389 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1389 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389 ,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,