RetrogeneDB ID: retro_opri_1037

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6084:54145..54613(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSOPRG00000006006
• Aliases: None
• Description: serine/arginine-rich splicing factor 3 [Source:HGNC Symbol;Acc:10785]

Sequence

>retro_opri_1037
ATGCATCGTGATTCCTGTCCATTGGACTGTAAGGTTTACTTAGGTAATCTTGGAAACAATGGCAATAAGACTGAATTGCA
ACGAACTTTTGGCCACTCTGAAGTGTATGGGTTGCAAGAAACCGTCCTGGCTTTGCTTTTGTTGAATTCGAAGACCCCTG
GGTTGCAGCTGATGCTGATGGTGTCCGTGAGCCAGCTGGAGGAACACCCTGTGGCTGTCCTGTGAGAGTGGAGCAGTGGA
CTGGCGAAAAAAGAAGTCAAAATAGTGGTCCACCTCTCTTTCGGGGCCTTTGCCCTCGAGACGATTAGCATACAAATCCT
CCACCTCCATGCAGATCTCCAAGAAGGAAAAGCTTCTCTTGCAGCCGGAGAGGGCCCTTTCTAGGGACAAGAGAACAGAA
AGATAAATGTCTGCGAGAGAAATCACAAGTCATCCCGATCCTTCTCTAAATCTGGGTCAAAAGAAAGA

Alignment

ORF - retro_opri_1037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.41 %
• Parental protein coverage: 96.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYG-PLRSVWVARNPPGFAFVEFEDPRDAADA--VRELD
          MHRDSCPLDCKVY...LGN.GN...........G.PL.SVWVARN.PGFAFVEFEDP..AADA..VRE..
Retrocopy MHRDSCPLDCKVY---LGNLGNNGNKTELQRTFG<PL*SVWVARNRPGFAFVEFEDPWVAADADGVREPA

Parental  GRTLCGCRVRVELSNGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSR-SRSLSRDRRRE
          G.T.CGC.VRVE...GEKRS.N.GPP...G..PRDD.....PPP..RSPRR.SFS.SR..R.LSRD.R.E
Retrocopy GGTPCGCPVRVEQWTGEKRSQNSGPPLFRGLCPRDD-*HTNPPPPCRSPRRKSFSCSR<ERALSRDKRTE

Parental  RSLSR-ERNHKPSRSFSRSRSRSR
          R..S..ERNHK.SRSFS.S.S..R
Retrocopy R*MSA<ERNHKSSRSFSKSGSKER

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_1037 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 18 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000040006	5 retrocopies	retro_btau_1176, retro_btau_1442, retro_btau_1445, retro_btau_1665, retro_btau_1813,
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Homo sapiens	ENSG00000112081	4 retrocopies	retro_hsap_2140, retro_hsap_2299, retro_hsap_2304, retro_hsap_757,
Loxodonta africana	ENSLAFG00000018193	2 retrocopies	retro_lafr_1219, retro_lafr_80,
Microcebus murinus	ENSMICG00000004674	5 retrocopies	retro_mmur_1090, retro_mmur_160, retro_mmur_287, retro_mmur_710, retro_mmur_916,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Mustela putorius furo	ENSMPUG00000014215	1 retrocopy	retro_mputfur_613,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
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,
Rattus norvegicus	ENSRNOG00000000520	11 retrocopies	retro_rnor_1010, retro_rnor_1283, retro_rnor_1321, retro_rnor_1339, retro_rnor_1647, retro_rnor_1697, retro_rnor_1889, retro_rnor_2424, retro_rnor_634, retro_rnor_728, retro_rnor_790,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,
Tarsius syrichta	ENSTSYG00000013498	3 retrocopies	retro_tsyr_1867, retro_tsyr_2163, retro_tsyr_848,
Tursiops truncatus	ENSTTRG00000013447	11 retrocopies	retro_ttru_105, retro_ttru_1195, retro_ttru_1577, retro_ttru_1628, retro_ttru_1639, retro_ttru_1653, retro_ttru_1677, retro_ttru_1731, retro_ttru_1892, retro_ttru_610, retro_ttru_916,
Vicugna pacos	ENSVPAG00000005481	1 retrocopy	retro_vpac_541,