RetrogeneDB ID: retro_dord_793

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_994:122124..122976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rbmxl1
• Ensembl ID: ENSDORG00000015481
• Aliases: None
• Description: RNA binding motif protein, X linked-like-1 [Source:MGI Symbol;Acc:MGI:1343045]

Sequence

>retro_dord_793
CCTCCAAGAAGCAGAGGTCCTCCCAGAGGTCTCAGAGGAGGAAGTGGTGGAACTAGAGGACCTGCCTCACGTGGAGGACA
CATGGATGATTTTAACATGAGTTCTTCCAGGGGGCCTCTTCCAGTGACAAGAGGCCCGCCACCACGAAGTGGGGGTCCCC
CTCCTAAGAGATCAGCACCTTCAGGACCAGTTCGCAGCAGCAGTGGAATGGGAGGGAGAGCCCCTGTATCACGTGGAAGA
GACAGTTATGGAGGCCCACCCCGAAGGGAACCCCTGCCTTCTCGAAGAGATGTTTATTTGTCCCCAAGAGATGATGGATA
GTCTACTAAAGATAGCTACTCAAGTAGAGATTACCCAAGTTCTCGGGACACAAGAGATTATGCGCCACCTCCAAGAGATT
ACACTTCCCGTGATTATGGTCATTCCAGTTCACGTGATGACTATCCGTCAAGAGGCTATAGTGATCGAGATGGATATGGT
CGGGATCGTCACTATTCAGATCATCCAAGTGGAGGCTCCTACAGAGATTCATATGAGAGTTATGGTAACTCACGTAGTGC
TCCACCTACACGAGGGCCCCCGCCATCTTACGGTGGAAGCAGTCGCTATGATGATTACAGCAGCTCACGAGACGGATATG
GTGGAAGTCGAGACAGTTACTCAAGCAGCCGAAGTGATCTCTACTCAAGTGGTCGTGATCGGGTTGGCAGACAAGAACGA
GGGCTTCCCCCGTCTATGGAAAGGGGGTACCCTCCTCCACGTGATTCTTACAGCAGTTCAAGCCGCCGAGCACCAAGAGG
TGGTGGCCGTGGAGGAAGCCGATCTGATAGAGGGGGAGGCAGAAGCAGATAC

Alignment

ORF - retro_dord_793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.59 %
• Parental protein coverage: 89.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNMSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSS
          PPR.....RG..GG..G.....G....GG....FNMSSSRGPLPV.RGPPPRSGGPPPKRSAPSGPVRSS
Retrocopy PPRSRGPPRGLRGGSGGTR---GPASRGGHMDDFNMSSSRGPLPVTRGPPPRSGGPPPKRSAPSGPVRSS

Parental  SGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYR
          SGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPRDDG.STKDSYSSRDYPSSRDTRDYAPPPRDYT.R
Retrocopy SGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPRDDG*STKDSYSSRDYPSSRDTRDYAPPPRDYTSR

Parental  DYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGSYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYS
          DYGHSSSRDDYPSRGYSDRDGYGRDR.YSDHPSGGSYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYS
Retrocopy DYGHSSSRDDYPSRGYSDRDGYGRDRHYSDHPSGGSYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYS

Parental  SSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLPPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDR
          SSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLPPSMERGYPPPRDSYSSSSR.APRGGGRGGSRSDR
Retrocopy SSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLPPSMERGYPPPRDSYSSSSRRAPRGGGRGGSRSDR

Parental  GGGRSRY
          GGGRSRY
Retrocopy GGGRSRY

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_793 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.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
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,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,