RetrogeneDB ID: retro_dnov_1944

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_38220:38260..38847(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSDNOG00000009228
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]

Sequence

>retro_dnov_1944
ATGTCTAAGTCAGAGTTTCATAAGGAGCCTGAACAGCAGTGGAAGCTCTTCATCAGAGGATTAAGTTTTGAAATAACCAA
TAAGATTCTGAGGAGCTATTCTGAGAAATGGAGAACAGTCACAGACTGTGTGGTAATGATAGGTCCAAACACCAAGCGTT
CCAGAGGCTTTGGGTTTGTCACATATGCCAGTGCGGAGGAAGTGGATGTATGCCATGAACGCAAGGCTGTACAAGCTGGA
TGGAAGAGCTATGAAACCAAAGAGGGCTGTCTCAAGAGAAGATTCCCAAAGACCAAGTGCCCACTTAACTATGAAAAAGA
TCTTGGTTGGTGGTATTAAAGAAGACACGGAAGAGCATCACCTAAGAGATTATTTTGAGCAGTATAGGAAAATTGATGTA
ATTGAAATCATGACTGACTGAGGTAGTGGCAAGAAGAGAAGTTTTTGCTTTTGTAATCTTTGACGACCATGACTCTGTGG
GTAAGGCTGTTATTCAGAAATACCATATCATGAATGGCCACAATTGTGAAGTAAGGAAAGTCCTGTCTAGGCAAGAGATG
GCCAGTGCTTCATCCAGCCAAAGAGGT

Alignment

ORF - retro_dnov_1944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.19 %
• Parental protein coverage: 52.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
          MSKSE..KEPEQ..KLFI.GLSFE.T...LRS..E.W.T.TDCVVM..PNTKRSRGFGFVTYA..EEVD.
Retrocopy MSKSEFHKEPEQQWKLFIRGLSFEITNKILRSYSEKWRTVTDCVVMIGPNTKRSRGFGFVTYASAEEVDV

Parental  -AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
          .AMNAR..K.DGR...PKRAVSREDSQRP.AHLT.KKI.VGGIKEDTEEHHLRDYFEQY.KI.VIEIMTD
Retrocopy >AMNARLYKLDGRAMKPKRAVSREDSQRPSAHLTMKKILVGGIKEDTEEHHLRDYFEQYRKIDVIEIMTD

Parental  RGSGKKRG-FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRG
          .GSGKKR..FAFV.FDDHDSV.K.VIQKYH..NGHNCEVRK.LS.QEMASASSSQRG
Retrocopy *GSGKKRS>FAFVIFDDHDSVGKAVIQKYHIMNGHNCEVRKVLSRQEMASASSSQRG

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	177.55 RPM
SRP012922_cerebellum	0.00 RPM	128.12 RPM
SRP012922_heart	0.00 RPM	62.65 RPM
SRP012922_kidney	0.00 RPM	56.95 RPM
SRP012922_liver	0.00 RPM	49.54 RPM
SRP012922_lung	0.00 RPM	170.14 RPM
SRP012922_quadricep_muscle	0.00 RPM	55.21 RPM
SRP012922_spleen	0.00 RPM	188.75 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_1944 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.

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000717	3 retrocopies	retro_amel_1726, retro_amel_547, retro_amel_925,
Canis familiaris	ENSCAFG00000006580	16 retrocopies	retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360, retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
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,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Myotis lucifugus	ENSMLUG00000000648	3 retrocopies	retro_mluc_2503, retro_mluc_342, retro_mluc_82,
Macaca mulatta	ENSMMUG00000012989	5 retrocopies	retro_mmul_1031, retro_mmul_1427, retro_mmul_1726, retro_mmul_187, retro_mmul_1871,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Procavia capensis	ENSPCAG00000001867	5 retrocopies	retro_pcap_111, retro_pcap_162, retro_pcap_377, retro_pcap_424, retro_pcap_435,
Pongo abelii	ENSPPYG00000025850	4 retrocopies	retro_pabe_1765, retro_pabe_2285, retro_pabe_3492, retro_pabe_3835,
Ictidomys tridecemlineatus	ENSSTOG00000006551	8 retrocopies	retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
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,