RetrogeneDB ID: retro_dord_667

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_501:7925..8619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Srsf10
• Ensembl ID: ENSDORG00000009136
• Aliases: None
• Description: serine/arginine-rich splicing factor 10 [Source:MGI Symbol;Acc:MGI:1333805]

Sequence

>retro_dord_667
GGTCGTTATGGCCCTATAGTTGATGTGTATGTTCCACTTGATTTCTACCCTCGACGTCCAAGAGGATTTGCTTATGTTCA
ATTTGAGGATGTTCGTGATGCTGAAGATGCTTTCCAGAATTTGGACAGAAAGTGTATTTGTGGATGTCAAATTGAAATAC
AGTTTGCACAGGGAGATCGGAAGACACCAAACCAAATGAAAGCCAAGGAAGGGAGGAATGTGTACAGCTTCATGGTATGA
TGACTATGACAGATACAGACGTTCTAGAAGCCGAAGTTATATGAGTGGAGGAGATCAAGAAGTCTGTCTTTTGATTAAAT
ACAGAAGATCTTACAGTCCTAGAAACAGTAGACCGACTGGAAGACCACGGCGTAGCAGAAGCCATTCCGACAGTGATAGA
TTCAAACACCGAAATCCATCTTTTTCAACATCTAAATCTATTTCAAGATCATGGTCCAAGTCCCAGTCCAAGAAAAGAAA
TGAAGGCTAAATCTCATTCTATGTCTGCATCTCACACCAAAACTAGAAGCACCTCTCAAACAGATTCCAAAACACATTAT
AAGTCTGGCTCAAGATATAAAAAGGAATCAAGGAAAAAAGAACCACCTAGATCCAAATCTCAGTCAACATCACAGTCTAG
GTCTAGGTCAAAATCTAGATCAAGGTCGTGGACTAGTACTAAGTCAGTGGCCAC

Alignment

ORF - retro_dord_667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 88.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFAQGDRKTPNQMKA-K
          GRYGPIVDVYVPLDFY.RRPRGFAYVQFEDVRDAEDA..NLDRK.ICG.QIEIQFAQGDRKTPNQMKA..
Retrocopy GRYGPIVDVYVPLDFYPRRPRGFAYVQFEDVRDAEDAFQNLDRKCICGCQIEIQFAQGDRKTPNQMKA>R

Parental  EGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYRRSYSPRNSRPTGRPRRSRSHSDNDRFKHRN
          .G......S.YDDYDRYRRSRSRSY.............YRRSYSPRNSRPTGRPRRSRSHSD.DRFKHRN
Retrocopy KG-GMCTASWYDDYDRYRRSRSRSYMSGGDQEVCLLIKYRRSYSPRNSRPTGRPRRSRSHSDSDRFKHRN

Parental  RSFSRSKSNSRSRSKSQ-PKKEMKAKSRSRSASHTKTRSTSKTDSKTHYKSGSRYEKESRKK-PPRSKSQ
          .SFS.SKS.SRS.SKSQ.P.KEMKAKS.S.SASHTKTRSTS.TDSKTHYKSGSRY.KESRKK.PPRSKSQ
Retrocopy PSFSTSKSISRSWSKSQ>PRKEMKAKSHSMSASHTKTRSTSQTDSKTHYKSGSRYKKESRKKEPPRSKSQ

Parental  SRSQ--SSRKSRSRSWTSPKS-SGH
          S.SQ..S..KSRSRSWTS.KS.SGH
Retrocopy STSQSRSRSKSRSRSWTSTKS<SGH

Legend:

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

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_667 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Dipodomys ordii	ENSDORG00000009136	1 retrocopy	retro_dord_667 ,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Tupaia belangeri	ENSTBEG00000017716	1 retrocopy	retro_tbel_4154,