RetrogeneDB ID: retro_btau_813

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:28309924..28310355(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SC5DL
• Ensembl ID: ENSBTAG00000019246
• Aliases: None
• Description: lathosterol oxidase [Source:RefSeq peptide;Acc:NP_001030433]

Sequence

>retro_btau_813
TATTCCTTCTTTGCAACACTGAGTTATTATGTTGTCTATGATCTTTCCTTAATTAAAGACAATTTTTAAAGAATCAAGTC
TATTGATAGATTATGCATTCTGTCCAGCCAATGCCATGGATCAGCATCCCCATATTTCCTCCTTTCCTGCTAGAGGTGAC
AGGTTACAGCAAATTGTATAATGGCATAGGAGAGTTTCCATATAGTTGGTTTCAACTCATTGCTGGTATCTATTTTTCTC
TTTTTCACTGACATGCTGATCTACTGGATTCACAGAGGCTTTCATCAGAGACTTGTATATATAAGCGCTTACACAAACCT
CATCACATCTGGCAGGTTCTGACTTCATTTGTAAATCATGCTTTTCACCTTCTGGATGACGTCCTTCAGAGTCTGCCTTA
CCATAGATATCCTTTTATCTTTCCTTTAAAC

Alignment

ORF - retro_btau_813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.9 %
• Parental protein coverage: 74.36 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YFFFATLSYYFVYDHL-LMKHPQFLKNQVSREITHSVQSMPWMSIPTVLLFLLEVRGYSRLYDGIGEFPY
          Y.FFATLS.Y.V...L......QFLKNQV...I.HSVQ.MPW.SIP....FLLEV.GYS.LY.GIGEFPY
Retrocopy YSFFATLS-YYVVYDL<FLN*RQFLKNQVY**IMHSVQPMPWISIPIFPPFLLEVTGYSKLYNGIGEFPY

Parental  GWFQLVASVLSFLFFTDMLIYWIHRGLHHKLVYKRLHKPHHIWKIPTPFASHAFHPLDGFLQSLPYHIYP
          .WFQL.A.....LF..........R.......YKRLHKPHHIW...T.F..HAFH.LD..LQSLPYH.YP
Retrocopy SWFQLIAGIYFSLFH*HADLLDSQRLSSETCIYKRLHKPHHIWQVLTSFVNHAFHLLDDVLQSLPYHRYP

Parental  FIFPLH
          FIFPL.
Retrocopy FIFPLN

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	1244.52 RPM
ERP005899_muscle	0.00 RPM	38.38 RPM
SRP017611_brain	0.00 RPM	57.78 RPM
SRP017611_kidney	0.00 RPM	65.61 RPM
SRP017611_liver	0.00 RPM	239.14 RPM
SRP030211_testis	0.01 RPM	7.70 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_813 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_813 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019246	1 retrocopy	retro_btau_813 ,
Canis familiaris	ENSCAFG00000011805	1 retrocopy	retro_cfam_291,
Callithrix jacchus	ENSCJAG00000007436	1 retrocopy	retro_cjac_1911,
Monodelphis domestica	ENSMODG00000013028	1 retrocopy	retro_mdom_1086,
Mustela putorius furo	ENSMPUG00000005754	1 retrocopy	retro_mputfur_484,
Ochotona princeps	ENSOPRG00000003219	1 retrocopy	retro_opri_1143,
Ictidomys tridecemlineatus	ENSSTOG00000008946	1 retrocopy	retro_itri_964,
Tupaia belangeri	ENSTBEG00000000490	1 retrocopy	retro_tbel_4326,
Tarsius syrichta	ENSTSYG00000011139	1 retrocopy	retro_tsyr_1097,
Tursiops truncatus	ENSTTRG00000006908	1 retrocopy	retro_ttru_777,