RetrogeneDB ID: retro_dnov_1689

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_267311:56..1006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDO1
• Ensembl ID: ENSDNOG00000002167
• Aliases: None
• Description: indoleamine 2,3-dioxygenase 1 [Source:HGNC Symbol;Acc:6059]

Sequence

>retro_dnov_1689
ATAAACGAAGATGTGGGCTTTGCTCTGCTAGGTCCACTGGAGGGGTTGCCTAATAAGTATGCCGCCTGGATAGTCATTGT
TCAAAACGTGCCTGACCTGATTAAGACCAGCCAGTCATGCACAGAAGTTGAAAAGTTGCCAGAACTCAGCATTGATGAGC
TTGAAGGACACAAGTTGCAGCACCTTGCCCACCTGATCTTGGGGTAAATCACCACAGCCTACGTGTGGCATCAAGGTGCC
CAAGATGTCTGTAAGGTCCTGCCAAGAAATATTGCCATTCCTCACTGCAAAATCTTGGAGAAGTTGAGACTGCCTGTTAT
CCTGGTGTGTGCAGATTGTGTCTTGCAAACTGGAAGAAAAAGGACCCCGGTGGGCCCATGACTTATGAGAACATGGACAT
CCTCTTCTCCTTCCCTGGTGGAGACTGCAGAAAAGGTTGCTTCCTGGTGTCACTATTTGTGGAAATAGCAGCTGCTTCTG
CTATCAAAGAAATCCTGTTATACTCAATGCTAAACAATGTCAGGACCAGGGAACTGTGAAAACAGAACTGGAAAAAATAA
CTGATTCCCTGAAGAAAGCCTTGGAAGTATTGGCCAAATTGACATTACATGGACCCAAAGGTATTTTCCAATGTTCTTTG
CATCTGGAAAGGCACCTCCCAGCCGCCAGAAGGCCTGCTGTATGAAGGGGTCTGGGACACCCACAGCAATTTGCAGGGGG
CAGTACAGCCCAAAGCAGCACCTTTCAGGGCTTTGATGCCCTGCTGGGCATCCGGCAGTGTTGGTGGAGAACATGCTGCT
GAGTTTCTCCAGGAAATGAGAACATCTATGCCACCAGCTCACCAGGCCTCTCTTCGCTCATCAGAGACAGCCCCATCCGT
ACACAGGTTTGTCCTGTCCAAAGGAGATGCAGCTAACGATGAATGTGTGAAAGCTGTGGTCTCCTGGAGG

Alignment

ORF - retro_dnov_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.88 %
• Parental protein coverage: 81.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  INEDVGFALPDPLEELPKKYDDWMFIAQNLPDLIKTGKLREEVEKLPELSIDDLEGHKLQRLAHLVLGYI
          INEDVGFAL..PLE.LP.KY..W..I.QN.PDLIKT.....EVEKLPELSID.LEGHKLQ.LAHL.LG.I
Retrocopy INEDVGFALLGPLEGLPNKYAAWIVIVQNVPDLIKTSQSCTEVEKLPELSIDELEGHKLQHLAHLILG*I

Parental  TMAYVWDRGDQDVRKVLPRNIAIPYCRISEMLKLPPILSYADCV-LANWKKKDPSG---VKNMEILFSFP
          T.AYVW..G.QDV.KVLPRNIAIP.C.I.E.L.LP.IL..ADCV.LANWKKKDP.G.....NM.ILFSFP
Retrocopy TTAYVWHQGAQDVCKVLPRNIAIPHCKILEKLRLPVILVCADCV<LANWKKKDPGGPMTYENMDILFSFP

Parental  GGDCGKGFFLVSLLVEIAAASVIKEI-PILINAIQHQDQATVKTELEKITGCLKEALEAFTQF-HKYVDP
          GGDC.KG.FLVSL.VEIAAAS.IKEI.P...NA.Q.QDQ.TVKTELEKIT..LK.ALE......H.Y.DP
Retrocopy GGDCRKGCFLVSLFVEIAAASAIKEI<PVILNAKQCQDQGTVKTELEKITDSLKKALEVLAKL>H-YMDP

Parental  NNFFNILRIYLSGWKNSSKLPEGLLYEGVWDT-PKQFAGGSAGQSSTFQCFDALLGIRQ-IPGGQEAEFL
          ..F.N.L.I.....K..S..PEGLLYEGVWDT.P.QFAGGS..QSSTFQ.FDALLGIRQ...G...AEFL
Retrocopy KVFSNVLCIW----KGTSQPPEGLLYEGVWDT<PQQFAGGSTAQSSTFQGFDALLGIRQ>VGGEHAAEFL

Parental  QEMRTYMPPAHQAFLRSLESAPSVRKFVQSSGDPGLPAAYDECVNAMVSLR
          QEMRT.MPPAHQA.LRS.E.APSV..FV.S.GD....AA.DECV.A.VS.R
Retrocopy QEMRTSMPPAHQASLRSSETAPSVHRFVLSKGD----AANDECVKAVVSWR

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	3.50 RPM
SRP012922_cerebellum	0.00 RPM	0.14 RPM
SRP012922_heart	0.00 RPM	10.44 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.00 RPM	1.08 RPM
SRP012922_lung	0.15 RPM	411.75 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.58 RPM
SRP012922_spleen	0.00 RPM	29.42 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_1689 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002167	3 retrocopies	retro_dnov_1689 , retro_dnov_2547, retro_dnov_2609,