RetrogeneDB ID: retro_dnov_959

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_127295:3347..3946(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSDNOG00000019022
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_dnov_959
GAACATTTTGAGAAATGGGGCACACTCACAGATTGTGTGGTGATGATAGACCCCCAGACAAAATGTTCCAGAGGCTTTGG
TTTTGTGACTTACTCTTGTGTTGAAGAGGCGGATGCAGCAATGTGTGCTCATCCACACAAGGTTAACGGGCGTGTAGTGG
AACCAAAGAAAGCTGTTTCTAGAGAGGATTCTGTGAAGCCTGGTGCCCATCTAACAGTGAAGGAAATTTCTGTTGGTGGT
ATCCAAGAAGATACAGAAGAATATAACTTGAGAGACTACTCTGAAAAGTATGGCAAGATTGAAACCAGGGAAGTTATGGA
AGACAGGCAGAGTGGAAGAAAGAGAGGATGTGCATGTGTGACTTTTGATGATCATGATACAGCTGATAAAATTGTTGCTC
AGAAATACCACACTATTAATGGGCACAACTGTGAAGTGAGAAAGCCCTTTCTAAACAAGAGATGCACTCTGCTGGACCAA
AAGAGGTCATGGAGGTGGATCTGGCAACTTCATGGGTATGGAGGGATCTTTGGAGGAGGTAAAGGGACCTTTGGCCGTGT
GGAAACTTTGGTGGAAGAGGAGGCCATGGTGGTGGAGGT

Alignment

ORF - retro_dnov_959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.88 %
• Parental protein coverage: 53.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAH
          EHFEKWGTLTDCVVM.DPQTK.SRGFGFVTYSCVEE.DAAMCA.PHKV.GRVVEPK.AVSREDSVKPGAH
Retrocopy EHFEKWGTLTDCVVMIDPQTKCSRGFGFVTYSCVEEADAAMCAHPHKVNGRVVEPKKAVSREDSVKPGAH

Parental  LTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTIN
          LTVK.I.VGGI.EDTEEYNLRDY.EKYGKIET.EVMEDRQSG.KRG.A.VTFDDHDT.DKIV.QKYHTIN
Retrocopy LTVKEISVGGIQEDTEEYNLRDYSEKYGKIETREVMEDRQSGRKRGCACVTFDDHDTADKIVAQKYHTIN

Parental  GHNCEVK-KALSKQEMQSAG-SQRGRGGGSGNFMGR-GGNFGGGGGNFGR-GGNFGGRGGYGGGG
          GHNCEV..KALSKQEM.SAG...RG.GGGSGNFMG..GG.FGGG.G.FGR..GNFGGRGG.GGGG
Retrocopy GHNCEVR<KALSKQEMHSAG<TKRGHGGGSGNFMGM<GGIFGGGKGTFGR<CGNFGGRGGHGGGG

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	435.41 RPM
SRP012922_cerebellum	0.14 RPM	188.74 RPM
SRP012922_heart	0.00 RPM	84.00 RPM
SRP012922_kidney	0.00 RPM	178.51 RPM
SRP012922_liver	0.15 RPM	125.39 RPM
SRP012922_lung	0.00 RPM	212.44 RPM
SRP012922_quadricep_muscle	0.00 RPM	83.43 RPM
SRP012922_spleen	0.46 RPM	328.96 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_959 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 18 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
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 ,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,