RetrogeneDB ID: retro_btau_606

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:64127392..64127767(-)
• Located in intron of: ENSBTAG00000032151

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B14
• Ensembl ID: ENSBTAG00000003407
• Aliases: None
• Description: pre-mRNA branch site protein p14 [Source:RefSeq peptide;Acc:NP_001039482]

Sequence

>retro_btau_606
ATGGCAATGCAAGCGGCCAAGAGGGCGAACATTCGACTTCCACCAGAAGTAAATCAGATTTTGTATATAAGAAATTTGCC
TTACAAAATCACAGCTGAAGAAATGTATGATATATTTGGGAAATATGGACCTATTCGTCAAATCAGAGTGGGGAACACAC
CTGAAACTAGAGGAACAGCTTATGTGATCTATGAGGACATCTTTGATGCCAAGAATGCATGTGATCACCTGTCAGGATTC
AATGTTTGTAACAGATACCTTGTGGTTTTGTACTATAATGCCAACAGGGCATTTCAGAAGATGGACACAAAGAAGAAGGA
AGAACAGTTGAAGCTCCTTAAGGAGAAATATGGCATCAACACAGATCCACCAAAG

Alignment

ORF - retro_btau_606 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA
          MAMQAAKRANIRLPPEVN.ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYV.YEDIFDA
Retrocopy MAMQAAKRANIRLPPEVNQILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVIYEDIFDA

Parental  KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK
          KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK
Retrocopy KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK

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	1.23 RPM	34.10 RPM
ERP005899_muscle	0.05 RPM	44.18 RPM
SRP017611_brain	0.14 RPM	14.02 RPM
SRP017611_kidney	0.12 RPM	27.56 RPM
SRP017611_liver	0.08 RPM	22.27 RPM
SRP030211_testis	0.14 RPM	29.01 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_606 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_606 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606 ,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457, retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,