RetrogeneDB ID: retro_btau_837

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:119050743..119051406(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000005584
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SFRS9
• Ensembl ID: ENSBTAG00000012792
• Aliases: SRSF9, SFRS9
• Description: serine/arginine-rich splicing factor 9 [Source:RefSeq peptide;Acc:NP_001076867]

Sequence

>retro_btau_837
ATGTCGGGCTGGGAGGACGAGCGCGGCGGCGAGGGCGACGGGCGCATCTACGTGGGGAACCTTCCGAACGACGTGCGCGA
GAAGGATCTGGAGGACCTGTTCTACAAGTACGGCCACATCAGCGAGATCGAGCTCAAGAATCGGCACGGCCTCGTGCCCT
TCGCCTTCGTGCGCTTCGAGGACCCCCGAGATGCTGAGGATGCAGTTTATGGAAGGAACGGTTATGATTATGGCCAGTGT
CGGCTTCGTGTGGAGTTCCCCAGGACTTACGGAGGTCGGGGTGGGTGGCCCCGCGGTGGGAGGAGTGGGCCTCCTACAAG
AAGATCTGATTTCCGAGTTCTTGTTTCAGGACTTCCTCCATCAGGCAGCTGGCAGGACCTGAAGGATCACATGCGAGAAG
CTGGGGACGTCTGTTACGCAGATGTGCAGAAAGATGGAATGGGGATGGTTGAGTATCTCAGAAAAGAAGACATGGAATAT
GCCCTGCGTAAACTGGATGAAACCAAATTCCGCTCTCATGAGGGTGAAACATCCTACATCCGAGTTTATCCAGAGAGAAG
CACCAGCTATGGCTATTCACGGTCTCGGTCTGGGTCGAGGGGCCGTGACTCTCCATACCAAAGCAGGGGTTCCCCACACG
ACTTCTCTCCTTTCAGACCCTAC

Alignment

ORF - retro_btau_837 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGWADERGGEGDGRIYVGNLPSDVREKDLEDLFYKYGRISEIELKNRHGLVPFAFVRFEDPRDAEDAIY
          MSGW.DERGGEGDGRIYVGNLP.DVREKDLEDLFYKYG.ISEIELKNRHGLVPFAFVRFEDPRDAEDA.Y
Retrocopy MSGWEDERGGEGDGRIYVGNLPNDVREKDLEDLFYKYGHISEIELKNRHGLVPFAFVRFEDPRDAEDAVY

Parental  GRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRSGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA
          GRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRSGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA
Retrocopy GRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRSGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA

Parental  DVQKDGMGMVEYLRKEDMEYALRKLDETKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRG
          DVQKDGMGMVEYLRKEDMEYALRKLDETKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRG
Retrocopy DVQKDGMGMVEYLRKEDMEYALRKLDETKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRG

Parental  SPHYFSPFRPY
          SPH.FSPFRPY
Retrocopy SPHDFSPFRPY

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	0.22 RPM	14.20 RPM
ERP005899_muscle	0.16 RPM	26.50 RPM
SRP017611_brain	0.18 RPM	12.97 RPM
SRP017611_kidney	0.18 RPM	21.81 RPM
SRP017611_liver	0.15 RPM	11.78 RPM
SRP030211_testis	1.03 RPM	21.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_837 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_837 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837 ,
Bos taurus	ENSBTAG00000040006	5 retrocopies	retro_btau_1176, retro_btau_1442, retro_btau_1445, retro_btau_1665, retro_btau_1813,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,