RetrogeneDB ID: retro_dnov_1654

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_257306:555..1120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSDNOG00000014270
• Aliases: None
• Description: general transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:HGNC Symbol;Acc:20872]

Sequence

>retro_dnov_1654
GCGGCGGCAGAAGAGTAAAGTTGGGATGATGGGGAGGAGGAGGAAGAGGAAGCACAGCAGTTGGTTCTGATGGAATTGTC
AGGAATTACTGACTCAGACTTTCTCTCAAATGTGAAAATAAACGCAAGATTTGGGGAATTGACAGAGTGGCCCATTCTGA
AAATGGACAGCTATGTCTTTGGTGGGGAGTATTAAGACACACTTGGGACATGTTATATTTATAGAAAATGTGGAACATAT
GGATGCAGAAGGCAGTAATAAAACAGTGCTAAAATATAAATGTCATACAATGATCAAGTTCAGCATGACAAGAACTATTT
TGACAGAAAAGAAAGATAAGAAAACAGGTGTTGTGGAGTGGCTGTACATCAAAGATAACGATAGCTCCTCTATACCCAAC
ATGATTTGTAGCTTTATACATGAAAATGAAGATGAAGAAGTTGTAGCTCCAACCCCAGATAAACCATTGGAAGAGCAAGA
GATTCAAATGAAAGACAATTCAAACCTGAATTATGAACAGGGGAAACCACTGCACATGGAAATAGAGGATTCTGGTCCTC
TTATT

Alignment

ORF - retro_dnov_1654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.87 %
• Parental protein coverage: 90.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAAEERGRDGGEEEEE---QLVLMELSGIIDSDFLSKCENKCKILGIDTERPILQMDSYVFAGEYEDT-L
          AAAEE...D.GEEEEE...QLVLMELSGI.DSDFLS.........G..TE.PIL.MDSYVF.GEY.DT.L
Retrocopy AAAEE*SWDDGEEEEEEAQQLVLMELSGITDSDFLSNVKINARF-GELTEWPILKMDSYVFGGEY*DT>L

Parental  GTCVIFEENVEHVDAEGNNKTVLKYKYHTMKKLSMTRTLLTEKKEGEENIGGVEWLQIKDNDFSYRPNMI
          G..VIF.ENVEH.DAEG.NKTVLKYK.HTM.K.SMTRT.LTEKK......G.VEWL.IKDND.S..PNMI
Retrocopy GH-VIFIENVEHMDAEGSNKTVLKYKCHTMIKFSMTRTILTEKKD--KKTGVVEWLYIKDNDSSSIPNMI

Parental  CSFIHENEDEEVVAPAADKPLELEEQEIQMKDNSNLNYEQGKPLHLEIEDSGPLI
          CSFIHENEDEEVVAP..DKP..LEEQEIQMKDNSNLNYEQGKPLH.EIEDSGPLI
Retrocopy CSFIHENEDEEVVAPTPDKP--LEEQEIQMKDNSNLNYEQGKPLHMEIEDSGPLI

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	9.14 RPM
SRP012922_cerebellum	3.99 RPM	14.71 RPM
SRP012922_heart	1.16 RPM	9.28 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.15 RPM	7.28 RPM
SRP012922_lung	1.22 RPM	9.01 RPM
SRP012922_quadricep_muscle	0.35 RPM	6.92 RPM
SRP012922_spleen	1.83 RPM	14.99 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_1654 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 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003535	1 retrocopy	retro_amel_370,
Callithrix jacchus	ENSCJAG00000005248	2 retrocopies	retro_cjac_3118, retro_cjac_4098,
Dasypus novemcinctus	ENSDNOG00000014270	4 retrocopies	retro_dnov_1228, retro_dnov_1654 , retro_dnov_377, retro_dnov_931,
Homo sapiens	ENSG00000155115	3 retrocopies	retro_hsap_3714, retro_hsap_4728, retro_hsap_4735,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Myotis lucifugus	ENSMLUG00000013919	1 retrocopy	retro_mluc_897,
Macaca mulatta	ENSMMUG00000012709	3 retrocopies	retro_mmul_1700, retro_mmul_2520, retro_mmul_2524,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Nomascus leucogenys	ENSNLEG00000012846	3 retrocopies	retro_nleu_1237, retro_nleu_2122, retro_nleu_2552,
Pan troglodytes	ENSPTRG00000018502	3 retrocopies	retro_ptro_2516, retro_ptro_3145, retro_ptro_3149,