RetrogeneDB ID: retro_dnov_2360

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_67391:622..1215(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCB10
• Ensembl ID: ENSDNOG00000023785
• Aliases: None
• Description: ATP-binding cassette, sub-family B (MDR/TAP), member 10 [Source:HGNC Symbol;Acc:41]

Sequence

>retro_dnov_2360
AGTCTTTCTTTGCCATCGGGCTCTGTCACAGCACTGGTTGGCTGAAGAGGTGCTGGCAAATCAAAGTAGTTTTAGTCCTT
TTGAAGTTGTATGACCTCATTTCTGGAAATGTCAGTCTGGATGATTGTGACATTCATCAGCTACATCCAGTCTGATTGAG
AGCCAAGATTGGGACAGTGAGTTAGGAACCAATTTTATTTTCTTGCTCAGTTGCTGAGAACATAGCTTATAGCACAGACA
ACCCTGCCCTAGTGACTGCAGAACAGGCAGAGAACATGGTTGATGTAGCAAATGCATCTGCTTTCATTAAATATTTCCCC
TAAAGATTCAACACTGTGATTGGAGAAAAGGGTGTTCTCCTTTCAGGTGGACATAAACAGTGGATTGTACCTGCCTATAC
TCTGCTTAAGAATCCCCAAATTCTTCTCCTGGATGAAGCATTTAGTACAGTGGATGCTGAAAATGAATTTCTTGTACAAG
AAGCTCTAGATTGCCTAATGGAAGGAAGATCAGTGTTAGTTATTGCCCATTGTCTGTCCACAATTAATGCTAATATGGTT
GCTGTTCTTAAGCAAGGAAAAGTTAGTGAATAT

Alignment

ORF - retro_dnov_2360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71. %
• Parental protein coverage: 51.55 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLRIPAGSVTALVGPSGSGKST-VVSLLLRLYDPVSGTVSLDGCDIRQLNPVWLRSKIGTVSQEPILFSC
          SL..P.GSVTALVG..G.GKS..VV..LL.LYD..SG.VSLD.CDI.QL.PV.LR.KIGTVS.EPILFSC
Retrocopy SLSLPSGSVTALVG*RGAGKSK<VVLVLLKLYDLISGNVSLDDCDIHQLHPV*LRAKIGTVS*EPILFSC

Parental  SIAENIAYGADDPALVTAEQVEKVADVANAAAFIRNFPQGFSTVVGEKGVLLSGGQKQRIAIARALLKNP
          S.AENIAY..D.PALVTAEQ.E...DVANA.AFI..FP..F.TV.GEKGVLLSGG.KQ.I..A..LLKNP
Retrocopy SVAENIAYSTDNPALVTAEQAENMVDVANASAFIKYFP*RFNTVIGEKGVLLSGGHKQWIVPAYTLLKNP

Parental  KILLLDEATSALDAENEHLVQEALDRLMEGRTVLVIAHRLSTVKRAHRVAVLSQGRIAEY
          .ILLLDEA.S..DAENE.LVQEALD.LMEGR.VLVIAH.LST...A..VAVL.QG...EY
Retrocopy QILLLDEAFSTVDAENEFLVQEALDCLMEGRSVLVIAHCLSTI-NANMVAVLKQGKVSEY

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	16.92 RPM
SRP012922_cerebellum	0.00 RPM	31.34 RPM
SRP012922_heart	0.00 RPM	14.62 RPM
SRP012922_kidney	0.00 RPM	22.18 RPM
SRP012922_liver	0.00 RPM	22.60 RPM
SRP012922_lung	0.00 RPM	42.15 RPM
SRP012922_quadricep_muscle	0.00 RPM	46.73 RPM
SRP012922_spleen	0.00 RPM	244.26 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_2360 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011011	1 retrocopy	retro_cjac_3824,
Dasypus novemcinctus	ENSDNOG00000023785	1 retrocopy	retro_dnov_2360 ,
Homo sapiens	ENSG00000135776	3 retrocopies	retro_hsap_1470, retro_hsap_1537, retro_hsap_1542,