RetrogeneDB ID: retro_dnov_377

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4228:55854..56354(-)
• Located in intron of: ENSDNOG00000004816

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_377
TTGGACACTGAGAGGCCCAGTGTGCAATGGACAGCTGTGCTTTGCCGGGGAGTATGAAGGCACTCTTGGGTCCTGTGTTA
TGTTTGAAGAAAATTTAGCACATGTGGATGCAAAAGGTAATAAAAAAAAAACAATGCTAAAATATAAGTGACTTACAACC
AAGAAGCTCAGCATGGCAAGAATTCCTCTGATAGAAAAGAAAGGAGAAGAAAAAAATAAGTGATATGGGTTGGCTGCAAA
GCAAAGATAATGATTTATCCTATAGACTTAACATGTTTTGAAGTTTTTTACATGAAAATGTAGATGAAGAAGTTATAGCT
CTGACTCAGATAAACCTTTAGAGTTGCAAGCGGAAGAGATCCAAATGAAAGACAATTCAAACCTCAATTATGAACAGCAG
AAACCACTGCACTTGTAAACAGAGGATTCTGGTCATCTTATTGATATCCCTTCTTCTGAGACAGAAGGTTCTGCTTTGAT
GGAAGCTCAAGATGCTGCCT

Alignment

ORF - retro_dnov_377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.63 %
• Parental protein coverage: 79.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IDTERPILQ-MDSYV-FAGEYEDTLGTCVIFEENVEHVDAEGNNKT-VLKYKYHTMKKLSMTRTLLTEKK
          .DTERP..Q.MDS...FAGEYE.TLG.CV.FEEN..HVDA.GN.....LKYK..T.KKLSM.R..L.EKK
Retrocopy LDTERPSVQ<MDSCA<FAGEYEGTLGSCVMFEENLAHVDAKGNXXXXMLKYK*LTTKKLSMARIPLIEKK

Parental  EGEEN-IGGVEWLQIKDNDFSYRPNMICSFIHENEDEEVVAPA-ADKPLELEEQEIQMKDNSNLNYEQGK
          .GEE..I....WLQ.KDND.SYR.NM..SF.HEN.DEEV.A....DKPLEL...EIQMKDNSNLNYEQ.K
Retrocopy -GEEK>ISDMGWLQSKDNDLSYRLNMF*SFLHENVDEEVIALT<SDKPLELQAEEIQMKDNSNLNYEQQK

Parental  PLHLEIEDSGPLIDIPSSETEDFVLMETQ-MLP
          PLHL..EDSG.LIDIPSSETE...LME.Q.MLP
Retrocopy PLHL*TEDSGHLIDIPSSETEGSALMEAQ>MLP

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	9.14 RPM
SRP012922_cerebellum	0.00 RPM	14.71 RPM
SRP012922_heart	0.00 RPM	9.28 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.00 RPM	7.28 RPM
SRP012922_lung	0.00 RPM	9.01 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.92 RPM
SRP012922_spleen	0.00 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_377 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,