RetrogeneDB ID: retro_btau_387

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:104175770..104176772(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000007516
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAT2B
• Ensembl ID: ENSBTAG00000012350
• Aliases: None
• Description: Methionine adenosyltransferase 2 subunit beta [Source:UniProtKB/Swiss-Prot;Acc:Q29RI9]

Sequence

>retro_btau_387
ATGGTGGGCCGGGAGAAAGAGCTCTCTATCCACTTTGTTCCCGGGGACTGCCGGTTGGTGGAGGAGGAAGTTAACATCCC
CAACAGGCGCGTTCTCATTACTGGTGCCACTGGGCTTTTTGGCAGAGCTGTGTACAAAGAATTTCAGCAGAATAATTGGC
ATGCCGTTGGCTGTGGTTTTAGAAGAGCAAGACCAAAATTTGAGCAGGTCAATCTCTTGGATTCTAATGCAGTTCATCAC
ATCATTTATGATTTTCAGCCCCATGTCATCGTACACTGTGCAGCAGAGAGAAGGCCAGATGTTGTAGAAAATCACCCAGA
TACTGCTTCTCAACTTAATGTGGATGCTTCTGGGAATTTAGCAAAGGAAGCAGCTGCAATTGGAGCATTTCTAATCTACA
TTAGCTCTGATTATGTTTTTGATGGAACAAACCCACCTTATAGAGAGGAAGACATACCAAATCCCCTAAATCTATATGGC
AAAACAAAATTAGAAGGAGAAAAGGCCGACCTGGAGAACAATTTAGGAGCTGCTGTTTTGAGAATTCCTGTTCTGTATGG
AGAAGTTGAAAGGCTTGAGGAAAGTGCTGTGACTATTATGTTTGATAAAGTGCAGTTCAGCAACAAGTCCGCAAACATGG
ACCACTGGCAGCAACGGTTCCCCACGCACGTCAAAGATGTGGCCACCGTGTGTCGTCAGTTAGCAGAGAAGAGGATGCTG
GATCCATCAATTAAGGGAACCTTTCACTGGTCTGGCAACGAACAGATGACTAAGTATGAAATGGCGTGTGCAATTGCAGA
TGCCTTCAACCTCCCCAGCAGCCACTTAAGACCGATAACTGACAGTCCTGTCGTAGGAGCACACCGTCCGAGAAATGCTC
AGCTTGATTGCTCTAGATTGGAGACCTTGGGCATTGGCCAGCGAACACCATTTCGAATTGGAATCAAAGAGTCACTCTGG
CCTTTCCTGATTGACAAGAGATGGAGACAGACGGTCTTTCAT

Alignment

ORF - retro_btau_387 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVGREKELSIHFVPGDCRLVEEEVNIPNRRVLITGATGLLGRAVYKEFQQNNWHAVGCGFRRARPKFEQV
          MVGREKELSIHFVPGDCRLVEEEVNIPNRRVLITGATGL.GRAVYKEFQQNNWHAVGCGFRRARPKFEQV
Retrocopy MVGREKELSIHFVPGDCRLVEEEVNIPNRRVLITGATGLFGRAVYKEFQQNNWHAVGCGFRRARPKFEQV

Parental  NLLDSNAVHHIIYDFQPHVIVHCAAERRPDVVENHPDAASQLNVDASGNLAKEAAAIGAFLIYISSDYVF
          NLLDSNAVHHIIYDFQPHVIVHCAAERRPDVVENHPD.ASQLNVDASGNLAKEAAAIGAFLIYISSDYVF
Retrocopy NLLDSNAVHHIIYDFQPHVIVHCAAERRPDVVENHPDTASQLNVDASGNLAKEAAAIGAFLIYISSDYVF

Parental  DGTNPPYREEDIPNPLNLYGKTKLEGEKAVLENNLGAAVLRIPVLYGEVERLEESAVTIMFDKVQFSNKS
          DGTNPPYREEDIPNPLNLYGKTKLEGEKA.LENNLGAAVLRIPVLYGEVERLEESAVTIMFDKVQFSNKS
Retrocopy DGTNPPYREEDIPNPLNLYGKTKLEGEKADLENNLGAAVLRIPVLYGEVERLEESAVTIMFDKVQFSNKS

Parental  ANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPIT
          ANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPIT
Retrocopy ANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPIT

Parental  DSPVVGAQRPRNAQLDCSRLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH
          DSPVVGA.RPRNAQLDCSRLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH
Retrocopy DSPVVGAHRPRNAQLDCSRLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH

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	0.07 RPM	10.89 RPM
ERP005899_muscle	0.21 RPM	37.43 RPM
SRP017611_brain	0.18 RPM	14.11 RPM
SRP017611_kidney	0.18 RPM	40.36 RPM
SRP017611_liver	0.08 RPM	5.59 RPM
SRP030211_testis	0.27 RPM	12.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_387 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_387 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	ENSBTAG00000012350	1 retrocopy	retro_btau_387 ,
Callithrix jacchus	ENSCJAG00000015401	1 retrocopy	retro_cjac_1749,
Macaca mulatta	ENSMMUG00000013980	1 retrocopy	retro_mmul_2019,
Ictidomys tridecemlineatus	ENSSTOG00000009459	1 retrocopy	retro_itri_1696,
Tursiops truncatus	ENSTTRG00000001154	1 retrocopy	retro_ttru_1573,