RetrogeneDB ID: retro_btau_1156

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:21867761..21868711(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000036111
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSBTAG00000020106
• Aliases: None
• Description: AP-2 complex subunit mu [Source:UniProtKB/Swiss-Prot;Acc:Q3ZC13]

Sequence

>retro_btau_1156
GGCTACCCACAGAACTCGGAGACAGGTGCACTGAAACCTTCATCACCCAGCAGGGGATCAAAAGCCAGCATCAGACAAAA
GAAGAGCAGTCTCAGATCACCAGCCAGGTGACTGGGCAGATTGGCTGGCGGCTGGAGGGCATCAAGTATCGCCGGAATGA
GCTCTTCCTGGATGTGCTGGAGAGTGTGAACCTCCTCATGTCCCCGCAAGGGCAGGTCCTGAGCGCCCATGTGTCAGGCC
GGGTAGTGATGAAGAGCTATCTGAGTGGCATGCCTGAGTGCAAGTTTGGAATGAATGACAAGATCGTCATTGAGAAGCAA
GGCAAAGGCACAGCTGATGAAACAAGCAAGAGCGGGAAGCAATCAATTGCCATTGATGACTGCACCTTCCACCAGTGTGT
GCGACTCAGCAAGTTTGATTCTGAACGCAGCATCAGCTTTATCCCACCAGATGGAGAATTTGAACTCATGAGGTATTGCA
CCACCAAGGACATCATCCTTCCTTTTCGCGTGATCCCACTAGTTCGGGAAGTGGGACGCACCAAGCTGGAGGTCAAGGTG
GTCATTAAGTCCAACTTCAAACCCTCACTACTGGCTCAGAAGATTGAGGTGCGGATCCCAACCCCACTGAACACTAGTGG
GGTGCAGGTAATCTGCATGAGGGGGAAGGCCAAGTATAAGGCCAGTGAGAACGCCATCGTGTGGAAGATCAAGCGCATGG
CAGGCATGAAGGAATCGCAAATCAGCGCTGAAATTGAGCTGCTGCCCACCAACGACAAGAAGAAATGGGCTCGACCCCCC
ATTTCAATGAACTTTGAGGTGCCATTCGCACCTTCTGGTCTCAAGGTGCGCTACTTGAAGGTGTGTGAACCGAAGCTGAA
CTACAGCGACCACGATGTCATCAAATGGGTGCGCTACATTGGCCGCAGCGGCATTTATGAGACCCGCTGC

Alignment

ORF - retro_btau_1156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.43 %
• Parental protein coverage: 72.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYPQNSETGALK-TFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSP
          GYPQNSETGALK.TFITQQGIKSQHQTKEEQSQITSQVTGQIGWR.EGIKYRRNELFLDVLESVNLLMSP
Retrocopy GYPQNSETGALK<TFITQQGIKSQHQTKEEQSQITSQVTGQIGWRLEGIKYRRNELFLDVLESVNLLMSP

Parental  QGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKF
          QGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKF
Retrocopy QGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKF

Parental  DSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTP
          DSERSISFIPPDGEFELMRY.TTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTP
Retrocopy DSERSISFIPPDGEFELMRYCTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTP

Parental  LNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPS
          LNTSGVQVICM.GKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPS
Retrocopy LNTSGVQVICMRGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPS

Parental  GLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC
          GLKVRYLKV.EPKLNYSDHDVIKWVRYIGRSGIYETRC
Retrocopy GLKVRYLKVCEPKLNYSDHDVIKWVRYIGRSGIYETRC

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	0.72 RPM	59.91 RPM
ERP005899_muscle	1.27 RPM	245.21 RPM
SRP017611_brain	5.76 RPM	330.03 RPM
SRP017611_kidney	3.02 RPM	169.40 RPM
SRP017611_liver	1.96 RPM	99.97 RPM
SRP030211_testis	0.53 RPM	95.32 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1156 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020106	1 retrocopy	retro_btau_1156 ,
Canis familiaris	ENSCAFG00000012257	2 retrocopies	retro_cfam_1923, retro_cfam_2028,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Mus musculus	ENSMUSG00000022841	2 retrocopies	retro_mmus_1873, retro_mmus_1914,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Otolemur garnettii	ENSOGAG00000012286	1 retrocopy	retro_ogar_1110,
Rattus norvegicus	ENSRNOG00000001709	1 retrocopy	retro_rnor_2342,
Tursiops truncatus	ENSTTRG00000008493	1 retrocopy	retro_ttru_522,