RetrogeneDB ID: retro_dnov_2031

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_43238:13839..14351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTI1B
• Ensembl ID: ENSDNOG00000003643
• Aliases: None
• Description: vesicle transport through interaction with t-SNAREs 1B [Source:HGNC Symbol;Acc:17793]

Sequence

>retro_dnov_2031
TTTAAGAAGCTGCACAAAATCTTCCGCAGTCTCCTTGAGGATCTACGAGGGGTGCCAGAGCAGCTGCTGGGGGCGGCAGG
GACTGAAGAGAAGAAGTTGATCAGAGATTTTGATGAAAAGCAACAGGAAGGCAAATGAAATGCTGGCAGAGATGGAGAAG
GAACTACGTCATGCACCCCTATCTTTCTGCAACCTCATGATGTCCAAGCTTCAAACCTACAAGAAGGACCTTGGTAAATT
CCATCGGGAGGGGGAGAAGCACACCTTTGACAGCCACACCTGGGGACCAAGGAGATATGAAATACAGCACATATGTGATG
GAAAATGAGCATATGAATTGGCAACAGTCTCAGAGAGCATTGGATCTGCTAGGCACTGACAGCCTGAACTGAGCCACCCA
GAGTACTGAGTGTTCTCATTGGATTGCCACAGAGACTGACCAGATTGGCTCAGAAATCATAGAGGAGCTCAGAGAACAAT
GAGAACAGTTGGAATGTACTAAGACTAGAGTG

Alignment

ORF - retro_dnov_2031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.66 %
• Parental protein coverage: 73.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FEKLHEIFRGLLEDLR-VPERLLGTAGTEEKKKLIRDFDEKQQE-ANETLAEMEKELRYAPLSFRNPMMS
          F.KLH.IFR.LLEDLR.VPE.LLG.AGTEEKK.LIRDFDEKQQE.ANE.LAEMEKELR.APLSF.N.MMS
Retrocopy FKKLHKIFRSLLEDLRGVPEQLLGAAGTEEKK-LIRDFDEKQQE>ANEMLAEMEKELRHAPLSFCNLMMS

Parental  KLRTYKKDLGKLHREV-RSTPLTATPGGRGDMKYGTYVVENEHMNWQQSQRALLLQGTDSLNRATQSIER
          KL.TYKKDLGK.HRE..RSTPLTATPG..GDMKY.TYV.ENEHMNWQQSQRAL.L.GTDSLN.ATQS.E.
Retrocopy KLQTYKKDLGKFHREG>RSTPLTATPGDQGDMKYSTYVMENEHMNWQQSQRALDLLGTDSLN*ATQSTEC

Parental  SHRIATETDQIGSEIIEELGEQREQLERTKTRL
          SH.IATETDQIGSEIIEEL.EQ.EQLE.TKTR.
Retrocopy SHWIATETDQIGSEIIEELREQ*EQLECTKTRV

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	0.00 RPM	50.56 RPM
SRP012922_cerebellum	0.00 RPM	51.41 RPM
SRP012922_heart	0.00 RPM	71.47 RPM
SRP012922_kidney	0.00 RPM	67.63 RPM
SRP012922_liver	0.00 RPM	25.85 RPM
SRP012922_lung	0.00 RPM	48.72 RPM
SRP012922_quadricep_muscle	0.00 RPM	55.21 RPM
SRP012922_spleen	0.00 RPM	53.68 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_2031 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 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015263	1 retrocopy	retro_cjac_1439,
Dasypus novemcinctus	ENSDNOG00000003643	2 retrocopies	retro_dnov_1503, retro_dnov_2031 ,
Dipodomys ordii	ENSDORG00000015939	2 retrocopies	retro_dord_52, retro_dord_716,
Echinops telfairi	ENSETEG00000006101	1 retrocopy	retro_etel_783,
Felis catus	ENSFCAG00000014090	1 retrocopy	retro_fcat_1855,
Homo sapiens	ENSG00000100568	3 retrocopies	retro_hsap_1002, retro_hsap_2682, retro_hsap_3013,
Gorilla gorilla	ENSGGOG00000005620	2 retrocopies	retro_ggor_1871, retro_ggor_797,
Macropus eugenii	ENSMEUG00000004910	2 retrocopies	retro_meug_499, retro_meug_697,
Microcebus murinus	ENSMICG00000010843	1 retrocopy	retro_mmur_849,
Myotis lucifugus	ENSMLUG00000011184	3 retrocopies	retro_mluc_1299, retro_mluc_2393, retro_mluc_781,
Macaca mulatta	ENSMMUG00000015866	1 retrocopy	retro_mmul_1420,
Mustela putorius furo	ENSMPUG00000007130	1 retrocopy	retro_mputfur_1516,
Nomascus leucogenys	ENSNLEG00000000780	4 retrocopies	retro_nleu_1184, retro_nleu_2241, retro_nleu_231, retro_nleu_83,
Pongo abelii	ENSPPYG00000005927	5 retrocopies	retro_pabe_2298, retro_pabe_2498, retro_pabe_2602, retro_pabe_845, retro_pabe_974,
Pan troglodytes	ENSPTRG00000006468	3 retrocopies	retro_ptro_1808, retro_ptro_2037, retro_ptro_751,
Pteropus vampyrus	ENSPVAG00000011671	3 retrocopies	retro_pvam_132, retro_pvam_592, retro_pvam_797,
Tupaia belangeri	ENSTBEG00000003049	1 retrocopy	retro_tbel_3432,
Tarsius syrichta	ENSTSYG00000007688	2 retrocopies	retro_tsyr_1662, retro_tsyr_94,