RetrogeneDB ID: retro_btau_111

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:13581142..13581886(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000022427
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PEX11A
• Ensembl ID: ENSBTAG00000006140
• Aliases: None
• Description: Peroxisomal membrane protein 11A [Source:UniProtKB/Swiss-Prot;Acc:Q0VCP2]

Sequence

>retro_btau_111
ATGGACGCCTTCATCCGCTTCACCAACCAGACCCAGGGCCGGGACCGACTCTTCAGAGCCACTCAGTACACATGCACGTT
GCTTAGATATTTGTTAGAGCCTAAAGCTGACAATGAGAAGGTTGTAATGAAGCTCAAGAAACTGGAATCCAGTGTGAGCA
CTGGCCGTAAATGGTTCAGACTAGGCAATGTGGTGCATGCTCTCCAGGCGACACAGCAGAGCGTTCGTGCCACTGACCTG
GTGCCCCGCATATGCCTAACAGTAGCCAGCTTGAACCGTGTGATTTATTTCATCCGTGACACCGTCCTCTTCGTGAGGAG
TACAGGGCTCGCCTCTGGTGTTAACAAAGAGAAATGGCGAAGGTGGGCTGCCCGCTATTACTACTATTCTCTTCTGCTGA
GCCTGGTCAGAGATCTGTACGAAGTCTCCCTGCAGCTGAAACAGGTTGCACACGACAGGGCAAAGAGGGAGAAGTCACCA
TCCCAGGATACCCTCGGGTACAGTGTGGCTGACGACGAGACAGAGTGGCTCCAGTCCCTTCTTCTTCTCTTATTCCACTC
TCTGAAGAGGCATCCTCCCTTGTTTCTGGACACAGTGAAGAACTTCTGTGACATCCTGAACCCCTTGGACCAGTTGGGGA
TCTATAAATCCAATCCTGGCATCATAGGCCTCGGAGGCCTCGTGTCCTCTGTAGCAGGCATCATCACTGTGGCGTATCCG
CAGATGAAACTGAAGACCCAGTGA

Alignment

ORF - retro_btau_111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAFIRFTNQTQGRDRLFRATQYTCMLLRYLLEPKADNEKVVMKLKKLESSVSTGRKWFRLGNVVHALQA
          MDAFIRFTNQTQGRDRLFRATQYTC.LLRYLLEPKADNEKVVMKLKKLESSVSTGRKWFRLGNVVHALQA
Retrocopy MDAFIRFTNQTQGRDRLFRATQYTCTLLRYLLEPKADNEKVVMKLKKLESSVSTGRKWFRLGNVVHALQA

Parental  TQQSVRATDLVPRICLTLASLNRVIYFICDTVLFVRSTGLASGVNKEKWRRWAARYYYYSLLLSLVRDLY
          TQQSVRATDLVPRICLT.ASLNRVIYFI.DTVLFVRSTGLASGVNKEKWRRWAARYYYYSLLLSLVRDLY
Retrocopy TQQSVRATDLVPRICLTVASLNRVIYFIRDTVLFVRSTGLASGVNKEKWRRWAARYYYYSLLLSLVRDLY

Parental  EVSLQMKQVAHDRAKREKSPSQDTLGYSVADEETEWLQSLLLLLFHSLKRHPPLFLDTVKNFCDILNPLD
          EVSLQ.KQVAHDRAKREKSPSQDTLGYSVAD.ETEWLQSLLLLLFHSLKRHPPLFLDTVKNFCDILNPLD
Retrocopy EVSLQLKQVAHDRAKREKSPSQDTLGYSVADDETEWLQSLLLLLFHSLKRHPPLFLDTVKNFCDILNPLD

Parental  QLGIYKSNPGIIGLGGLVSSVAGIITVAYPQMKLKTQ
          QLGIYKSNPGIIGLGGLVSSVAGIITVAYPQMKLKTQ
Retrocopy QLGIYKSNPGIIGLGGLVSSVAGIITVAYPQMKLKTQ

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	0.14 RPM	3.17 RPM
ERP005899_muscle	0.00 RPM	12.46 RPM
SRP017611_brain	0.00 RPM	5.48 RPM
SRP017611_kidney	0.00 RPM	9.31 RPM
SRP017611_liver	0.00 RPM	2.49 RPM
SRP030211_testis	0.04 RPM	8.91 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_111 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM482601	13581249	13581405	98.8	152	2	148

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_111 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	ENSBTAG00000006140	1 retrocopy	retro_btau_111 ,
Dasypus novemcinctus	ENSDNOG00000014344	1 retrocopy	retro_dnov_11,
Tupaia belangeri	ENSTBEG00000004185	1 retrocopy	retro_tbel_2910,
Tursiops truncatus	ENSTTRG00000015532	1 retrocopy	retro_ttru_412,