RetrogeneDB ID: retro_btau_1010

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:32385305..32386035(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000008491
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VAPB
• Ensembl ID: ENSBTAG00000017424
• Aliases: None
• Description: Vesicle-associated membrane protein-associated protein B [Source:UniProtKB/Swiss-Prot;Acc:A2VDZ9]

Sequence

>retro_btau_1010
ATGGCGAAGGTGGGGCAGGTCCTGAGCCTCGAGCCGCAGCACGAGCTCAAATTCCGAGGTCCCTTCACCGATGCTGTCAC
CACCAACCTGAAGCTTGGCAACCCGACAGATCGAAATGTGTGTTTTAAAGTGAAGACCACGGCACCACGTAGGTACTGCG
TGAGGCCCAACAGCGGGATCATTGATGCAGGGGCCTCGATTAACGTATCTGTGATGTTACAGCCTTTCGATTATGATCCC
AATGAGAAAAGTAAACACAAGTTTATGGTTCAGTCTATGTTTGCTCCAATTGACACTTCTGATATGGAAGCAGTATGGAA
GGAGGCAAAACCGGAAGACCTTATGGATTCAAAACTTAGATGTGTGTTTGAATTGCCAGCAGAAAATGATAAACCATATG
ATGTAGAAATAAATAAAATTATACCCACAACTGCATCAAAGACAGAAACACCAAAGGTGTCTAAAGCTCTGAGTTCCTCC
TTGGATGACACTGAAGTTAAGAAGGTGATGGAAGACTGTAAGAGGCTGCAGAGCGAAGTCCAGAGGCTGTGGGAGGAGGA
CAAGCAGTTCAAGGAGGAAGACGGACTTCTGATGAGGAAGACAGTGCAGAGCCACAGTCCCTGCTCCCGCGTCAGCCACG
GCTGGGAAGGAGGAGGGCCTGAGCACCGGGCTGCTGGCGCTCGGCGTCCTCTTCTTCATCGTTGGCGTGATCATAGGGAA
GACCGTCTTG

Alignment

ORF - retro_btau_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVS
          MAKV.QVLSLEPQHELKFRGPFTD.VTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVS
Retrocopy MAKVGQVLSLEPQHELKFRGPFTDAVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVS

Parental  VMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHDVEINKI
          VMLQPFDYDPNEKSKHKFMVQSMFAP.DTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKP.DVEINKI
Retrocopy VMLQPFDYDPNEKSKHKFMVQSMFAPIDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPYDVEINKI

Parental  IPTTASKTETPTVSKALSSSLDDTEVKKVMEECKRLQSEVQRLREENKQFKEEDGLRMRKTAQSNS-PAP
          IPTTASKTETP.VSKALSSSLDDTEVKKVME.CKRLQSEVQRL.EE.KQFKEEDGL.MRKT.QS.S.PAP
Retrocopy IPTTASKTETPKVSKALSSSLDDTEVKKVMEDCKRLQSEVQRLWEEDKQFKEEDGLLMRKTVQSHS>PAP

Parental  ASAMAGKEEGLSTRLLALVVLFFIVGVIIGKIAL
          ASA.AGKEEGLST.LLAL.VLFFIVGVIIGK..L
Retrocopy ASATAGKEEGLSTGLLALGVLFFIVGVIIGKTVL

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	32.01 RPM
ERP005899_muscle	0.05 RPM	73.69 RPM
SRP017611_brain	0.14 RPM	74.32 RPM
SRP017611_kidney	0.06 RPM	76.99 RPM
SRP017611_liver	0.15 RPM	50.44 RPM
SRP030211_testis	0.18 RPM	17.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1010 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1010 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1010 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017424	1 retrocopy	retro_btau_1010 ,
Dasypus novemcinctus	ENSDNOG00000012711	1 retrocopy	retro_dnov_206,
Macropus eugenii	ENSMEUG00000009788	1 retrocopy	retro_meug_842,
Monodelphis domestica	ENSMODG00000016549	1 retrocopy	retro_mdom_919,
Nomascus leucogenys	ENSNLEG00000009351	1 retrocopy	retro_nleu_55,