RetrogeneDB ID: retro_btau_1675

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:50574573..50575472(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046056
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.88309
• Ensembl ID: ENSBTAG00000020316
• Aliases: AP2B1, CLAPB1
• Description: AP-2 complex subunit beta [Source:RefSeq peptide;Acc:NP_001068593]

Sequence

>retro_btau_1675
ATGACTGACTCCAAGTACTTCACAACCAATAAAAAGGGAGAAATCTTTGAATTAAAAGCTGAACTCAACAATGAAAAGAA
AGAAAAGAGGAAGGGGGCTGTGAAGAAACTGATTGCTGCTATGACTGTGGGGAAAGATGTTAGCACTCTCTTTCCAGATA
TAGTGAACTATATGCAGACAGACAACCTGGAACTGAAGAAGCTTGTGTATCTCTACTTGATGAACTATGCCAAGAGTCAG
CCAGACATGGCCATCATGGCTGTCAACAGCTTTGTGAAGGACTGTAAAGATCCCAATCCTCTGACTCAAGCCTTGGCAGT
CAGAACCATGCAGTGCATCCGGATGAACAAGATTACAGAATATCTCTGTGAGCCCCTCTGCAAGTGCTTAAAGGATGATG
ATCCCTACGTCCAGAAGACAGCAGCAGTCTGTGTGGCAAAACTCCATAACATCAACGCCCAGATGATGGAAGATCAGGAA
TTTCTGGATTCTCTGTGGGATCACATAGCAGATTCAAATCCAATGATGGTAGCTAATGCTGTAGCAGCATTATCTGAAAT
CAGTGAATCTCACCCGAACATCAACTTACTCGATCTATATCCACAGAATATTAATAAGCTACTGACAGCCCTGAATGAGT
GCACTGAATGGGGCCAGATTTTCACCCTGGACTGCCTGTTTAATTACAATCCTAAAGATGACCGGGAGGCTCAGAACATC
TGTGAGCGGATAACTCCCTGGTTATCTCATGCCAACTCAGCAGTGGTGCTTTAGCAGTAAAAATCCTAATGAAATTTCTA
GAGTTTCTACCCAAGGACTCTGACTACTACAATATGCTGCTGAAGAAGTTGGCCCCTCCACTTGTCACTTGGCTGTCTGG
GGAGCCAGAGGTGCAATAC

Alignment

ORF - retro_btau_1675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.04 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDSKYFTTNKKGEIFELKAELNNEKKEKRK.AVKK.IAAMTVGKDVS.LFPD.VN.MQTDNLELKKLVY
Retrocopy MTDSKYFTTNKKGEIFELKAELNNEKKEKRKGAVKKLIAAMTVGKDVSTLFPDIVNYMQTDNLELKKLVY

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQPDMAIMAVNSFVKDC.DPNPL..ALAVRTM.CIR..KITEYLCEPL.KCLKD.DPYV.KT
Retrocopy LYLMNYAKSQPDMAIMAVNSFVKDCKDPNPLTQALAVRTMQCIRMNKITEYLCEPLCKCLKDDDPYVQKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLH.INAQM.EDQ.FLDSL.D.IADSNPM.VANAVAALSEISESHPN.NLLDL.PQNINKLLTA
Retrocopy AAVCVAKLHNINAQMMEDQEFLDSLWDHIADSNPMMVANAVAALSEISESHPNINLLDLYPQNINKLLTA

Parental  LNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVL-SAVKVLMKFLELLPKESDYYNM
          LNECTEWGQIF.LDCL.NYNPKDDREAQ.ICER.TP.LSHANSAVVL..AVK.LMKFLE.LPK.SDYYNM
Retrocopy LNECTEWGQIFTLDCLFNYNPKDDREAQNICERITPWLSHANSAVVL<LAVKILMKFLEFLPKDSDYYNM

Parental  LLKKLAPPLVTLLSGEPEVQY
          LLKKLAPPLVT.LSGEPEVQY
Retrocopy LLKKLAPPLVTWLSGEPEVQY

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	4.04 RPM
ERP005899_muscle	0.00 RPM	48.94 RPM
SRP017611_brain	0.05 RPM	122.06 RPM
SRP017611_kidney	0.06 RPM	95.96 RPM
SRP017611_liver	0.00 RPM	19.18 RPM
SRP030211_testis	0.10 RPM	706.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1675 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020316	1 retrocopy	retro_btau_1675 ,
Choloepus hoffmanni	ENSCHOG00000010864	1 retrocopy	retro_chof_2310,
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mustela putorius furo	ENSMPUG00000014910	1 retrocopy	retro_mputfur_704,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925, retro_nleu_2554,