RetrogeneDB ID: retro_itri_1205

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393400.1:4559797..4560461(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMX
• Ensembl ID: ENSSTOG00000006211
• Aliases: None
• Description: RNA binding motif protein, X-linked [Source:HGNC Symbol;Acc:9910]

Sequence

>retro_itri_1205
GCTGATGGGCCTGGGAGACTTTTCATAGGAGACCTCAATACAGAGACCAGAAAAAAAAAAAAGACTCCTGAAGTAGTATT
TGGGAAATTTGGAGTATATAGGAAATTCTTTTGATGAAAGCCAGGGAAACCAAGTCCAGAAGCTTTGCTGGTATTACTTT
TCAAAGCCCAGCTGATGCTAAAGATGCTGCCAAAGATACGAATGGAAAGTCTTTGCATGGAAAAACAATTAAAGGAGAGA
GAGCCAACAAACCATCGTTTGAGGGTGGTAGTAGGTGAAGACTACCATCTCTTTCAAGAAACAGAGGGCCTCCAAGAAGC
CTGAGATGTGGCAGAGGAGGAAGTGGAGGAACAAGATGGCGTCCTTCACGTGCAGGACACTTGGATGATGATGGATATAC
TCTGAATCTCAGCGTGAGTTCTTCTAGGGGGCCGTTTCCTGTTAAAAGAGGTCCAACTTCAAGAAGTAGAGATCCTCCTC
TTAAAGATCTGGTCCATCTGCTCCAACCAAGAGCAAGAGTAGTGTGGGAGGATGAGGTCCCCGGGTCTCCTGGGAGAGAG
AATTATGGAGAGGGCCATGCAGAGAACAAGTCTCTTCTCGGAGAGATGATTATGTGTCACCGAGAGATGCTGGTTACTCT
GCTAAAGATAGTTATGCAAGCAGA

Alignment

ORF - retro_itri_1205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.0 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ADRPGKLFIGGLNTETNEKAL--EAVFGKYG-RIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
          AD.PG.LFIG.LNTET.......E.VFGK.G..I.E.LLMK.RET.KSR.FA..TF.SPADAKDAA.D.N
Retrocopy ADGPGRLFIGDLNTETXXXXXTPEVVFGKFG<SI*EILLMKARET-KSRSFAGITFQSPADAKDAAKDTN

Parental  GKSLDGKAIKVEQATKPSFESGRR-GPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMHFN
          GKSL.GK.IK.E.A.KPSFE.G.R...P...R.RGPPR.LR.GRGGSGGTR..PSR.GH.DD.GY.....
Retrocopy GKSLHGKTIKGERANKPSFEGGSR*RLPSLSRNRGPPRSLRCGRGGSGGTRWRPSRAGHLDDDGYTLNLS

Parental  MSSSRGPLPVKRGPPPRSGGPPPK-RSAPSGPVRSSSGMGG-RAPVSRGRDSYG-GPPRREPLPSRRDVY
          .SSSRGP.PVKRGP..RS..PP.K.RS.PS.P..S.S..GG...P.S.GR..YG...P.RE...SRRD.Y
Retrocopy VSSSRGPFPVKRGPTSRSRDPPLK<RSGPSAPTKSKSSVGG>EVPGSPGRENYG<RGPCREQVSSRRDDY

Parental  LSPRDDGYSTKDSYSSR
          .SPRD.GYS.KDSY.SR
Retrocopy VSPRDAGYSAKDSYASR

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1205 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1205 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 22 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205 , retro_itri_1346,
Ictidomys tridecemlineatus	ENSSTOG00000006720	2 retrocopies	retro_itri_1807, retro_itri_776,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,