RetrogeneDB ID: retro_btau_1327

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:90164476..90165069(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BT.58955
• Ensembl ID: ENSBTAG00000007817
• Aliases: None
• Description: lys-63-specific deubiquitinase BRCC36 [Source:RefSeq peptide;Acc:NP_001069258]

Sequence

>retro_btau_1327
ATGGCAGTGCCGGTGGTGCAGGCTGTGAGAGCAGTTCATCTGGATGCTTTCCTAGTATGTCTCAATCACATGTCAGCACA
GAGAGGGAGGAGGTGATGGGGTTGTGCATAGGGGCGTTGAATGGTGATTTAAGTAGTGACTTCAAATTTACACGTATTGG
AACTTAAATCTGTATAGTTGCTGAAAAGTTGACATCAACATAAGTGTTCATGTTCATTTTGTCATCATCTTGCAATGTTC
TGATAAGAGGAAGGATAGAGTGGAAATTTCTCCAAATAGTTGTCTGTGGCCTCAACAGAGGCAGAGAAGTTGGCTGAACT
AACAGGTCACCCCATGAGAGTTGCAGGCTGGTATCATTCCCATCCCCATATAACTGTTTGGCCTTCACTTGTTGATTTTC
ACACCAAGCCATGTACCAGATGATGGATCAAGGCATTGTCAAGCTTATATTTTCCTGTTTCATAGGAGGTAAATGTACAA
AGACTGGATGGGTAATCTATACTTGCTTTCAATCCATACAGGTCCAAAAGAGCTCAGAATATGAGTGAATTGGAATCCCA
GTTTATATTGTACCTCATGTGACTATTGGAGAA

Alignment

ORF - retro_btau_1327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.66 %
• Parental protein coverage: 69.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAVQVVQAVQAVHLESDAFLVCLNHA-LSTEKEEVMGLCIGELNDDLRNDPKFTYTGTEMRTVAEK-VDT
          MAV.VVQAV.AVHL..DAFLVCLNH...STE.EEVMGLCIG.LN.DL..D.KFT..GT....VAEK.VD.
Retrocopy MAVPVVQAVRAVHL--DAFLVCLNHM<VSTEREEVMGLCIGALNGDLSSDFKFTRIGT*ICIVAEK<VDI

Parental  VRIVHIHSVIILRRSDKRKDRVEISPEQ-LSAASTETHRLAELTGRPMRVVGWYHSHPHITVWPSHVDVR
          ...VH.H.VIIL..SDKRKDRVEISP...LS.ASTE...LAELTG.PMRV.GWYHSHPHITVWPS.VD..
Retrocopy NISVHVHFVIILQCSDKRKDRVEISPNS<LSVASTEAEKLAELTGHPMRVAGWYHSHPHITVWPSLVDFH

Parental  T-QAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSEYERIEIPIHIVPHVTIGK
          T.QAMYQMMDQG.V.LIFSCFI..K.TKTG.V.YTCFQSIQ.QKSSEYE.I.IP..IVPHVTIG.
Retrocopy T<QAMYQMMDQGIVKLIFSCFIGGKCTKTGWVIYTCFQSIQVQKSSEYE*IGIPVYIVPHVTIGE

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	15.00 RPM
ERP005899_muscle	0.00 RPM	12.19 RPM
SRP017611_brain	0.00 RPM	11.15 RPM
SRP017611_kidney	0.00 RPM	14.28 RPM
SRP017611_liver	0.00 RPM	13.82 RPM
SRP030211_testis	0.00 RPM	1.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1327 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1327 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327 , retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,
Ictidomys tridecemlineatus	ENSSTOG00000019781	2 retrocopies	retro_itri_1271, retro_itri_806,