RetrogeneDB ID: retro_rnor_2339

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:154503177..154503746(+)
• Located in intron of: ENSRNOG00000005271

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hnrnpa2b1
• Ensembl ID: ENSRNOG00000011175
• Aliases: Hnrnpa2b1, Hnrpa2, Hnrpa2b1, hnRNP
• Description: heterogeneous nuclear ribonucleoproteins A2/B1 [Source:RefSeq peptide;Acc:NP_001098083]

Sequence

>retro_rnor_2339
TCTGATAGGCAATCTGGAAAGCCAGGGGGCTTCACTTCTTACTTTTGATGCCCATGATCCTGTGGATAAAAGTATATTGC
AAACACATCCCACCACCAATGGTCACAATGCAGAAGTTAGAAAGGCACTGTCTAGACAAGAGACGCAGGAAGTCTGAAGC
TCTAGGACTGGAAGAGGAGCAAACTTTGGTTTGGGGGACTTGTTGTGGTGGTGGTGGCATTTTTTGGACCAGGATCAGAA
AGCAGCTTTAGGTGGGGATCTGATGGGTAAGCAAGTGGATGTGGATTTGGAGATGGTTATAATGGATCTGGGGGTGGCAA
TTTTAGAAGGAGCCCAGGTTAGGGAGGAGAAAGAGGAGGATGTGGTGGTGGAGGATCTGGATAGAGCAACCAGGATGGGG
GGCTGTTGGAGGTGGTTATGACCACCGTGGTGGAGGAAATTTTGGAAAGTATAACCAGCAACCTTCCAACTCTGCTCCAA
TGAAGAGTGGAAACTTTGGTGGTAGCAGGAACATGGGAGGAGCATACGGTGGAAGGAAATATGGTCCTAGAGGAAGTGGG
TGTGGTGGG

Alignment

ORF - retro_rnor_2339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.91 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TDRQSG-KKRGFGFV-TFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGD-
          .DRQSG.K.RG..F..TFD.HDPVDK..LQ...T.NGHNAEVRKALSRQE.QEV.SSR.GRG.NFG.GD.
Retrocopy SDRQSG<KARGLHFL<TFDAHDPVDKSILQTHPTTNGHNAEVRKALSRQETQEV*SSRTGRGANFGLGD>

Parental  SRGGGG-NFGPGPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQG
          ..GGGG..FGPG..S.FR.GSDG..SG.GFGDGYNG.GGG....NF..SPG.GG.RGG.GGGG.G..NQ.
Retrocopy CCGGGG>FFGPGSESSFRWGSDG*ASGCGFGDGYNGSGGG----NFRRSPG*GGERGGCGGGGSG*SNQD

Parental  GGY-GGG-YDNYGGGNYGSGNYNDFGNYNQQPSNYGPMKSGNFGGSRNMGGPYGGGNYGPGG
          GG...GG.YD..GGGN.G..N............N.G...S.N.GG....G..YG....G.GG
Retrocopy GGL<VGGGYDHRGGGNFGKYNQQPSNSAPMKSGNFG--GSRNMGGAYG-GRKYGPRGSGCGG

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	236.54 RPM
SRP017611_kidney	0.00 RPM	315.97 RPM
SRP017611_liver	0.07 RPM	165.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2339 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2339 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Callithrix jacchus	ENSCJAG00000007908	2 retrocopies	retro_cjac_2285, retro_cjac_3041,
Ciona savignyi	ENSCSAVG00000000472	1 retrocopy	retro_csav_26,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077, retro_ogar_3189,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Rattus norvegicus	ENSRNOG00000011175	3 retrocopies	retro_rnor_1824, retro_rnor_2043, retro_rnor_2339 ,
Rattus norvegicus	ENSRNOG00000036839	17 retrocopies	retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,