RetrogeneDB ID: retro_ttru_1788

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_91619:2646..3446(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSTTRG00000000709
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_ttru_1788
AAAGCAGCGGCGGCGGCTCTAGCGGCAGTAGCAGTAGCGCCGGGTCCAGAGAGTGGAGGTGCTCCTAGAGCAGCGGCAGT
TCTGACTACAGCGCAGGGACGAGTCCGGTTCGTGTTCGTCCGCGGAGATCTCTCTCATCTCGCTCGGCTGCGGGAAATCG
GGCTGAAGCGACGGAGTCTGCGATGGAGAGAGAAAAGGAACAAATCCGTAAACTCTTTATTGGTGGCCTGAGCTTTGAAA
CTACAGAAGAAAGTTTGAAGAACTACTGCGAACAATGGGGGAAAACTTACAGACTGTGTGGTAATGAGGGATCCTGCAAG
CAAAAGATCATGAGGATTTCGTTTTGTAACTTTTTCATCCATGGCTGAGATCGATGCTGCCATGGCTGCCAGACCTCGTT
CAACTATGGGAGAGCGGTTGAACCAAAACATGCTGTTTGCAAGAGAGGAATCTGGAAAGCCAGGGGCTCATGTCACTCTG
AAGAAGCTGTTTGTAGGTGGAATTAAAGATGCTGAGGAACATTATCTTAGAGATTACTTTGAGGCATACGGACAAATTGT
TACCATTGAGATAATTACTGATAGGCAGTCTGGAAAGAAAAGAGGCTTTGGGTTTGTTACTTTTGATGAGCATGATCCTG
TGGATAAGAGTGTGTTGCAGAAATACCATACCATCAATGGTCATAATGCAGAAGTAAGAAAGGCTTTGTCTAGACAAGAA
ATGCAGGAAGTCCAAAGTTCTAGAAGTGGAAGAGGAGGCCACTTTGGTTTGGAGATTCTCGTGGTGCTGGTGGCAATTTT

Alignment

ORF - retro_ttru_1788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.39 %
• Parental protein coverage: 65.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RKAAAAALAAVAA-APGPEWRCSRCCFSTSGSSHYSARTSPVRVRPRRSLSSRSAAGNRAEATESAMERE
          ..AAAA..A...A.A...EWR....C...SGSS.YSA.TSPVRVRPRRSLSSRSAAGNRAEATESAMERE
Retrocopy KAAAAALAAVAVA<AGSREWR----CS*SSGSSDYSAGTSPVRVRPRRSLSSRSAAGNRAEATESAMERE

Parental  KEQFRKLFIGGLSFETTEESLRNYYEQWGK-LTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHS
          KEQ.RKLFIGGLSFETTEESL.NY.EQWGK.LTDCVVMRDPASKRS.GF.FVTFSSMAE.DAAMAARP.S
Retrocopy KEQIRKLFIGGLSFETTEESLKNYCEQWGK>LTDCVVMRDPASKRS*GFRFVTFSSMAEIDAAMAARPRS

Parental  IDG-RVVEPKRAV-AREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKR
          ..G.R.VEPK.AV.AREESGKPGAHVT.KKLFVGGIK.D.EEH.LRDYFE.YG.I.TIEIITDRQSGKKR
Retrocopy TMG<RAVEPKHAV>AREESGKPGAHVTLKKLFVGGIK-DAEEHYLRDYFEAYGQIVTIEIITDRQSGKKR

Parental  GFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFG-FGDSRGGGGNF
          GFGFVTFD.HDPVDK.VLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGG.FG.FGDSRG.GGNF
Retrocopy GFGFVTFDEHDPVDKSVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGHFG<FGDSRGAGGNF

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1788 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1788 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 20 parental genes, and 73 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	ENSDORG00000005482	1 retrocopy	retro_dord_489,
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 ,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,
Tursiops truncatus	ENSTTRG00000004505	27 retrocopies	retro_ttru_1202, retro_ttru_1223, retro_ttru_1251, retro_ttru_1331, retro_ttru_1362, retro_ttru_156, retro_ttru_157, retro_ttru_1678, retro_ttru_1732, retro_ttru_1806, retro_ttru_1813, retro_ttru_1874, retro_ttru_221, retro_ttru_311, retro_ttru_479, retro_ttru_599, retro_ttru_605, retro_ttru_607, retro_ttru_620, retro_ttru_63, retro_ttru_678, retro_ttru_708, retro_ttru_812, retro_ttru_882, retro_ttru_902, retro_ttru_926, retro_ttru_981,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,