RetrogeneDB ID: retro_dnov_476

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5145:236791..237491(+)
• Located in intron of: ENSDNOG00000007161

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABPA
• Ensembl ID: ENSDNOG00000016059
• Aliases: None
• Description: GA binding protein transcription factor, alpha subunit 60kDa [Source:HGNC Symbol;Acc:4071]

Sequence

>retro_dnov_476
GAGCCAGAATGCCTTGGGGTACCCTATGGTCCTACACAGTGGTTCACAGGCCAGGTCCTGCATTGGGTACTTGGGGAAAT
GAAGGAATCAACATAACTGATACAGACCTCACCTCCCTCAACATTCTGGGAAGAGAATTATGTGGTCTTATCCGTGAAGA
TTGTTTTCAGCGGATCCCTCAGGGAGAAATTCTCTGGAGTCATCTGGAGCGCCTTCGAAAACATGTAGTAGCAAGCCAAG
AACAACAGATGAATGAGATAGTTACAATTCATCAACCTGTGCAAATCATTCCAGCATCAGTGCAGTTGCTCTACCAACTA
CCATTAAAATTCCAAACAGTAGTGCAAAGGCAGCTAAAGTGCAGTGAGCTCCAAGGATTTCAGAAGATAGATGTACACGT
GGAAATAGGACAAGACACAATGACCAAATCCAGTTATGGCAATTATTGCTAGAACTTCTTACTGACAAGGATGCTAGAGA
GTGCATTTCTTGGGTTGGTGTTCAAGGTGAGTTTAGGCTAAATCAGCCTGAACTCGTTGCTCAGAAATGGGGACAATGTA
AAAATAAACTGACAATGAACTATGAGAAACTCAGCCATGCATTAAGGTATTATTATGATGGGGATATGATTTGTAAAATT
CAAGGTAAGAGATTTGTGTACAAATTCATCTATTTATCTCTTATTGGATACAGTGCAGCG

Alignment

ORF - retro_dnov_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.89 %
• Parental protein coverage: 55.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EQERLGIPYDPIQWSTDQVLHWVVWVMKE-FSMTDIDLTSLNISGRELCSLNQEDFFQRVPRGEILWSHL
          E.E.LG.PY.P.QW.T.QVLHWV...MKE....TD.DLTSLNI.GRELC.L..ED.FQR.P.GEILWSHL
Retrocopy EPECLGVPYGPTQWFTGQVLHWVLGEMKE<INITDTDLTSLNILGRELCGLIREDCFQRIPQGEILWSHL

Parental  ELLRKYVLASQEQQMNEIVTIDQPVQIIPASVQS-ATPTTIKVLNSSAKAAKVQRAPRISGEDRSSPGNR
          E.LRK.V.ASQEQQMNEIVTI.QPVQIIPASVQ..A.PTTIK..NSSAKAAKVQ.APRIS.EDR...GNR
Retrocopy ERLRKHVVASQEQQMNEIVTIHQPVQIIPASVQL<ALPTTIKIPNSSAKAAKVQ*APRIS-EDRCTRGNR

Parental  TGNNGQIQLWQFLLELLTDKDARDCISWVGDEGEFKLNQPELVAQKWGQRKNKPTMNYEKLSRALRYYYD
          T..N.QIQLWQ.LLELLTDKDAR.CISWVG..GEF.LNQPELVAQKWGQ.KNK.TMNYEKLS.ALRYYYD
Retrocopy TRHNDQIQLWQLLLELLTDKDARECISWVGVQGEFRLNQPELVAQKWGQCKNKLTMNYEKLSHALRYYYD

Parental  GDMICKVQGKRFVYKFVCDLKTLGYSTA
          GDMICK.QGKRFVYKF...L...GYS.A
Retrocopy GDMICKIQGKRFVYKFIY-LSLIGYSAA

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	8.95 RPM
SRP012922_cerebellum	0.00 RPM	4.40 RPM
SRP012922_heart	0.00 RPM	3.25 RPM
SRP012922_kidney	0.00 RPM	3.01 RPM
SRP012922_liver	0.00 RPM	4.33 RPM
SRP012922_lung	0.00 RPM	7.64 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.50 RPM
SRP012922_spleen	0.00 RPM	12.36 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_476 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013817	1 retrocopy	retro_cjac_2487,
Dasypus novemcinctus	ENSDNOG00000016059	1 retrocopy	retro_dnov_476 ,
Homo sapiens	ENSG00000154727	1 retrocopy	retro_hsap_3737,
Ochotona princeps	ENSOPRG00000009283	1 retrocopy	retro_opri_1174,
Pan troglodytes	ENSPTRG00000013810	1 retrocopy	retro_ptro_2536,
Tursiops truncatus	ENSTTRG00000004785	1 retrocopy	retro_ttru_154,