RetrogeneDB ID: retro_dord_651

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_48444:9351..10171(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Foxr1
• Ensembl ID: ENSDORG00000001960
• Aliases: None
• Description: forkhead box R1 [Source:MGI Symbol;Acc:MGI:2685961]

Sequence

>retro_dord_651
GCCAAATACAATCTCAGAATAGTTGAACCACCAGTATTGCCTCAGGATAAAAAGTATGAGGCTGATGAAGATGACCCAGA
TATTGAGCCCAACCTGTGGATGTGGGTAAATCCCAACATCTTGTACTCACCTGGCAAGATGCAGGTCAAAGAAGTTAAGT
GGGCACGTCCATCGAGCCTGCCTCTCACCTCCCAGTGATCTGTGAAGAAGGAAGAGGACAGCTGCTCAGAGGCTACAGAG
GAGCAATTGTAGCAGCCTTCCTCTAGCTTGTGGTCACCTTGTGAGAAGCCAAAGCTGAGCCCAGCTGCTTCCCCTCCCCC
TTGGCCCTGAGAGCTTGTGGAAGAGGAGGTAGCCCAGCACCAGGATGACAGCTTCTCTGTGGCCCTTGCATCTGCTCATC
TAGGACCACCTTCCAGAGTTGGATGCTCCGGCAGCCCATCAGCTCAGAGGGCAGGCTCTGGACCCGGCCCCCCTCAATGA
CTTCCACCTAATTGCCCTGGCACTAAGAAACAGTGCCCTCTGTGGCCTCAACGTGCAGCAGATCTAAAGCTTCACTCGAC
ACTTCCCCTTCTTCCAGATGGCTCCTGAAGGCTTTAAGAACATGGTCTGTCACAATCTCTGCTCCCAAGACAACTTTGAG
AAAGTGCCTATCAATATGAACGTGGAGGCTGGCACACAGCCTCGATCCTGCCTCTGGAAGCTGATGAAGGAGGGACACCG
CCACTTTCTGGAGGAGGCCGGTGTCTTGGCTTCCATTAGGACAGAACACATCCAACAGTGCATGAACTAGCAAGATATGA
TACCCTTCCTCTTTGACATT

Alignment

ORF - retro_dord_651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKYKLRIVEPPVLPLDKKYEADEDDPDIEPNLWMWVNPNIVYPPGKMQVKEAKWARPSSPPLASQRSVKK
          AKY.LRIVEPPVLP.DKKYEADEDDPDIEPNLWMWVNPNI.Y.PGKMQVKE.KWARPSS.PL.SQ.SVKK
Retrocopy AKYNLRIVEPPVLPQDKKYEADEDDPDIEPNLWMWVNPNILYSPGKMQVKEVKWARPSSLPLTSQ*SVKK

Parental  EEDSCSEATEEQLQQPSSSLGSPCEKQLAPP---PCPW--ELAEEEAAQHQDGSSSVALASAHLRGP-LQ
          EEDSCSEATEEQL.QPSSSL.SPCEK....P...P.PW..EL.EEE.AQHQD.S.SVALASAHL..P..Q
Retrocopy EEDSCSEATEEQL*QPSSSLWSPCEKPKLSPAASPPPWP*ELVEEEVAQHQDDSFSVALASAHLGPP<FQ

Parental  SRRLRQHISSEGRLWPRP-PLNYFHLIALALRNSPPCGLNVQQIYSFTRQHFPFFQTAPEGWKNTVRHNL
          S..LRQ.ISSEGRLW.RP.PLN.FHLIALALRNS..CGLNVQQI.SFTR.HFPFFQ.APEG.KN.V.HNL
Retrocopy SWMLRQPISSEGRLWTRP<PLNDFHLIALALRNSALCGLNVQQI*SFTR-HFPFFQMAPEGFKNMVCHNL

Parental  CFRDSFEKVPVNMNMEAGTRPRSCLWKLTEEGHRRFVEEARVLASTRMERIQQCMNQPDMMPFLFDL
          C..D.FEKVP.NMN.EAGT.PRSCLWKL..EGHR.F.EEA.VLAS.R.E.IQQCMN..DM.PFLFD.
Retrocopy CSQDNFEKVPINMNVEAGTQPRSCLWKLMKEGHRHFLEEAGVLASIRTEHIQQCMN*QDMIPFLFDI

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_651 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651 ,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,