RetrogeneDB ID: retro_dord_489

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22878:5076..5835(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hnrnpa2b1
• Ensembl ID: ENSDORG00000005482
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:MGI Symbol;Acc:MGI:104819]

Sequence

>retro_dord_489
AAGTCCGAGACTCCTAAGGAGCCCGAACAGCTGCGGAAGCTCTTCATCGGAGGGCTGAGCTTTGAAACGACCGATGAGAG
TCTGAGGAGCCATTTTGGGCCATGGGGAACCCTCACAGACTGTGTGGTAATGAGAGATCCCAACACCAAGCGCTCCAGGG
GCTTTGGGTTTGTAACTTATGCCACTGTGGAGGAAGTAGATGCAGCTATGAATGCAAGGCCACACAAAGTGGATGGAAGA
GTCGTGGAACCAAAAAGAGCCGTCTCAAGAGAAGATTCTCAGAGACCAGGTGCCCACTTAACTGTGAAGAAGATTTTTGT
TGGTGGCATTAAAGAAGACAGTGAAGAACACCATTTACGAGATTACTTTGAACAATATGGCAAAATTGAAGTGATTGAAA
TCATGACTGATCGAGGCAGTGGAAAGAAAAGAGGCTTTGCTTTTGTAACTCTTGATGACCATGACTCTGTGGACAAGATT
GTCATTCAGAAATACCATACAGTGAATGGCCACAACTGTGAAGTAAGGAAAGCCCTATCAAAGCAAGAGATGACTAGTGC
TTCTTCCAGCCAAAAAGGTTGAAGTGGTTCTGGAAACTTTGGTGGCAGTCGTGGAGGTGGTTTTGGTGGCAATGACAATT
TTGGTCGTGGAGGAAACTTCAGTGGTCGAGGTGGCTTTGGTGGCAGCCGTGGTGGTGGAGGATATGGCGGTAGTGGGGAT
GGCTACAATGGATTTGGTAATGATGGTAGCAATTTTGGA

Alignment

ORF - retro_dord_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 60.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESAMEREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM
          .S....E.EQ.RKLFIGGLSFETT.ESLR.....WG.LTDCVVMRDP..KRSRGFGFVT.....EVDAAM
Retrocopy KSETPKEPEQLRKLFIGGLSFETTDESLRSHFGPWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM

Parental  AARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQS
          .ARPH..DGRVVEPKRAV.RE.S..PGAH.TVKK.FVGGIKED.EEHHLRDYFE.YGKI..IEI.TDR.S
Retrocopy NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDSEEHHLRDYFEQYGKIEVIEIMTDRGS

Parental  GKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGG--GG
          GKKRGF.FVT.DDHD.VDKIV.QKYHT.NGHN.EVRKALS.QEM....SS..G..G...FG.SRGG..GG
Retrocopy GKKRGFAFVTLDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMTSASSSQKG*SGSGNFGGSRGGGFGG

Parental  NFGPGPGSNF--RGGSDGYGSGRGFG---DGYNGYGGGPGGGNFG
          N...G.G.NF..RGG..G...G.G.G...DGYNG.G....G.NFG
Retrocopy NDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGN--DGSNFG

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_489 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 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Choloepus hoffmanni	ENSCHOG00000013832	15 retrocopies	retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Ciona intestinalis	ENSCING00000004062	1 retrocopy	retro_cint_7,
Ciona savignyi	ENSCSAVG00000000472	1 retrocopy	retro_csav_26,
Dasypus novemcinctus	ENSDNOG00000012928	1 retrocopy	retro_dnov_1978,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145,
Dipodomys ordii	ENSDORG00000005482	1 retrocopy	retro_dord_489 ,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
Felis catus	ENSFCAG00000027765	1 retrocopy	retro_fcat_692,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Mus musculus	ENSMUSG00000004980	1 retrocopy	retro_mmus_573,
Oryctolagus cuniculus	ENSOCUG00000026859	2 retrocopies	retro_ocun_1205, retro_ocun_642,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Ictidomys tridecemlineatus	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,