RetrogeneDB ID: retro_btau_1089

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 25:26099150..26099847(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000032136
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.81335
• Ensembl ID: ENSBTAG00000002415
• Aliases: None
• Description: Tetraspanin-3 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZR9]

Sequence

>retro_btau_1089
GGAGCTGCTGGCATTTTATGCTATGTCAGAGCCTATGTCTTCATCACTTGCGACGACTATGACCACTTCTTTGAAGATGT
GTACACTCTCATCCCTGGTGTGGTGATCATAGCTGTCGGGGCCCTGGTCTTCATTATTGGGCTAATTGGTTGCTGTGCCA
CAATCCGGGAAAGCCGCTGTGGACTTGCCACGTTTGTCATCATCCTACTCTTGGGTTTTGTCACAGAAGTTGTTGTTGTG
GTTTTGGGATATGTTTACAGAGCAAAGGTGGAAAATGAAGTTGATCGCAGCATTCAGAAGGTGTATAAGACCTACAATGG
AACCAACCCTGATGCTGCTAGCCGGGGCCATTGACTGTGTTCAGAGACAGCTGCACTGTTGTGGAATTCACAACTATTCA
GACTGGGAAAATACAGACTGGTTCAAAGAAACCAAAAACCAGAGCGTCCCTCTTAGTTGTTGCAGAGAGACAGCCAGCAG
CTGTAACAGCAGCCTGGCCCACCGCTCTGATCTCTATGCTGAGGCGTGTGAGGCTCTAGTTGTGAAGAAGCTACAAGAAA
TCATGATGCATGTTATCTGGGCAGCATTGGCATTTGCAGCTATTCAGCTGCTGGGCATGCTGTGTGCCTGCATTGTGTTG
TGCAGAAGGAGTAGAGATCCTGCTTATGAGCTCCTCATCATCGGCGGAGCCTATGCA

Alignment

ORF - retro_btau_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAAGILCYVGAYVFITYDDYDHFFEDVYTLIPAVVIIAVGALLFIIGLIGCCATIRESRCGLATFVIILL
          GAAGILCYV.AYVFIT.DDYDHFFEDVYTLIP.VVIIAVGAL.FIIGLIGCCATIRESRCGLATFVIILL
Retrocopy GAAGILCYVRAYVFITCDDYDHFFEDVYTLIPGVVIIAVGALVFIIGLIGCCATIRESRCGLATFVIILL

Parental  LVFVTEVVVVVLGYVYRAKVENEVDRSIQKVYKTYNGTNPDAASR-AIDYVQRQLHCCGIHNYSDWENTD
          L.FVTEVVVVVLGYVYRAKVENEVDRSIQKVYKTYNGTNPDAASR.AID.VQRQLHCCGIHNYSDWENTD
Retrocopy LGFVTEVVVVVLGYVYRAKVENEVDRSIQKVYKTYNGTNPDAASR>AIDCVQRQLHCCGIHNYSDWENTD

Parental  WFKETKNQSVPLSCCRETASSCNGSLANPSDLYAEGCEALVVKKLQEIMMHVIWAALAFAAIQLLGMLCA
          WFKETKNQSVPLSCCRETASSCN.SLA..SDLYAE.CEALVVKKLQEIMMHVIWAALAFAAIQLLGMLCA
Retrocopy WFKETKNQSVPLSCCRETASSCNSSLAHRSDLYAEACEALVVKKLQEIMMHVIWAALAFAAIQLLGMLCA

Parental  CIVLCRRSRDPAYELLITGGAYA
          CIVLCRRSRDPAYELLI.GGAYA
Retrocopy CIVLCRRSRDPAYELLIIGGAYA

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	52.41 RPM
ERP005899_muscle	0.00 RPM	224.88 RPM
SRP017611_brain	0.09 RPM	63.54 RPM
SRP017611_kidney	0.00 RPM	51.15 RPM
SRP017611_liver	0.08 RPM	72.41 RPM
SRP030211_testis	0.07 RPM	96.13 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1089 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1089 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089 , retro_btau_1650,
Bos taurus	ENSBTAG00000011931	1 retrocopy	retro_btau_234,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,