RetrogeneDB ID: retro_opri_878

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_40026:7243..7817(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000006869
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSOPRG00000004234
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_opri_878
GACTGCACCGTCTACGTGGGAAACTTGCCCCCAGACATCAGAACGAAGGACGTCGAGGATGTGTTTTACAAATACGGCGC
TATCCGTGACATCGACCTCAAGAATCACCGCTGGGGACCGCCCTTCGCCTTCGTCGAGTTTGAGGACCGGCGGGACGCGG
AGGACGCGGTGTATGAGCGCGACGGCTACGATTTCGATGGGTACCGTCTCCGGGTGGAGTTTGCACGGAGCGGCCGCCGT
GCGGGGTGGATGGGGCCGAGCGCCATCCCGCTACGGCCCCCCATCCCGACGGTCTGACCATCGCGTGGTGGTCTCTGGGC
TGCCCCACACTGGAAGCTGGCAGGATCTAAAGGATCACATGCGTGAGGCAGGTGATATATGTTATGCCAATGTCCACGGA
GATGGCACCGGTGTCGTGGAGTTTGTACGGAAAGAAGGTATGACCTACGCAGTTCGAAAACTGGACAACACTAAGTTTAG
ATCTCACGTGGGAGAAGCTGCCTACATCCGGGTTAAAGCGGATGGGCCCAGAAGTCCCAGTTCTGGCAGATCTCCATCTC
GAAGCAGATCTCGT

Alignment

ORF - retro_opri_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.1 %
• Parental protein coverage: 85.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGRIYVGNLPTNVREKDLEDLFYKYGRIREIELKNRHGLVPFAFVRFEDPRDAEDAIYGRNGYDYGQCRL
          D...YVGNLP...R.KD.ED.FYKYG.IR.I.LKN.....PFAFV.FED.RDAEDA.Y.R.GYD....RL
Retrocopy DCTVYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNHRWGPPFAFVEFEDRRDAEDAVYERDGYDFDGYRL

Parental  RVEFPRT-YGSRGGWPRG-GRTGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMV
          RVEF.R.....RGGW.R...R.GPP.RRSD.RV.VSGLP..GSWQDLKDHMREAGD.CYA.V..DG.G.V
Retrocopy RVEFARS>AAVRGGWGRAPSRYGPPSRRSDHRVVVSGLPHTGSWQDLKDHMREAGDICYANVHGDGTGVV

Parental  EYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE--RSTSYGYSRSRSGSR
          E..RKE.M.YA.RKLD.TKFRSH.GE..YIRV.....RS.S.G.S.SRS.SR
Retrocopy EFVRKEGMTYAVRKLDNTKFRSHVGEAAYIRVKADGPRSPSSGRSPSRSRSR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_878 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
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	ENSOPRG00000001234	2 retrocopies	retro_opri_335, retro_opri_625,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878 ,
Ochotona princeps	ENSOPRG00000006006	3 retrocopies	retro_opri_1037, retro_opri_158, retro_opri_545,
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,