RetrogeneDB ID: retro_dnov_1978

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_40093:12417..13256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSDNOG00000012928
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_dnov_1978
GCAGCAGCGCCGGGGTCCGTGCGGAGCTGTTCCTAGCGGCGTTGTTTCTTGAGCAGCGGCAGTTCTCACAACAGCGCCAG
GACGAGTCCGGCTCGTGTTCGTCCGCGGAGATCTCTCTCATCTCGCTCGGCTGCGGGAAATCGGGCTGAAGCGACTGAGT
CCGCGATGGAGAGAGAAAAGGAACAATTCCGTAAACTCTTTATTGGTGGCTTAAGTTTTGAAACAACAGAAGAAAGTTTG
AGGAACTACTATGAGCAATGGGGAAAACTTACAGACTGTGTGGTGATGCGGGATCCTGCAAGTAAGAGATCAAGAGGATT
TGGTTTTGTAACTTTTTCATCCATGGCTGAGGTTGATGCTGCAATGGCTGCTAGACCTCATTCAATTGATGGGAGAGTGG
TTGAGCCGAAACGTGCTGTAGCAAGAGAGGAGTCTGGAAAACCAGGGGCTCATGTAACTGTGAAGAAGTTGTTTGTTGGT
GGAATTAAAGAAGATACTGAGGAACATCACCTTAGAGATTACTTCGAGGAATATGGAAAAATTGATACCATTGAGATAAT
TACTGATAGGCAATCTGGAAAGAAAAGAGGCTTTGGTTTTGTGACTTTTGATGACCATGATCCTGTTGATAAAATTGTAT
TGCAGAAATACCATACCATCAATGGTCATAATGCAGAAGTAAGAAAGGCTTTGTCTCGACAAGAAATGCAGGAAGTCCAA
AGTTCTAGAAGCGGAAGACGAGGCAATTTTGGTTTTGGAGATTCACGTGGTGGTGGTTGGAAATTTTGGACCAGGACCAG
GGAAGTAACTTTAGAGGAGGATCATATGGATATGGAAGT

Alignment

ORF - retro_dnov_1978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.22 %
• Parental protein coverage: 67.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAAPGSVRSCS-RRCFLSSGSSHNSARTSPARVRPRRSLSSRSAAGNRAEATESAMEREKEQFRKLFIGG
          AAAPGSVRSCS.RRCFLSSGSSHNSARTSPARVRPRRSLSSRSAAGNRAEATESAMEREKEQFRKLFIGG
Retrocopy AAAPGSVRSCS*RRCFLSSGSSHNSARTSPARVRPRRSLSSRSAAGNRAEATESAMEREKEQFRKLFIGG

Parental  LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV
          LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV
Retrocopy LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV

Parental  AREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVD
          AREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVD
Retrocopy AREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVD

Parental  KIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGGG-GNFGPGP-GSNFRGGSDGYG
          KIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGR.GNFGFGDSRGGG.GNFGPGP.GSNFRGGS.GYG
Retrocopy KIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRRGNFGFGDSRGGG>GNFGPGP>GSNFRGGSYGYG

Parental  S
          S
Retrocopy S

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
SRP012922_ascending_colon	0.19 RPM	487.92 RPM
SRP012922_cerebellum	0.69 RPM	500.25 RPM
SRP012922_heart	0.00 RPM	188.87 RPM
SRP012922_kidney	0.27 RPM	341.42 RPM
SRP012922_liver	0.93 RPM	267.97 RPM
SRP012922_lung	0.92 RPM	397.08 RPM
SRP012922_quadricep_muscle	0.17 RPM	281.95 RPM
SRP012922_spleen	0.57 RPM	486.00 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_1978 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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 19 parental genes, and 57 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	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Dasypus novemcinctus	ENSDNOG00000012928	1 retrocopy	retro_dnov_1978 ,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
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,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,