RetrogeneDB ID: retro_dnov_2324

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_64072:11749..12312(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GGCT
• Ensembl ID: ENSDNOG00000007242
• Aliases: None
• Description: gamma-glutamylcyclotransferase [Source:HGNC Symbol;Acc:21705]

Sequence

>retro_dnov_2324
ATGGTGGGCTTGGGCTGCAGGAATTGCCAGGGAAGGGACAAAGAGAATTTTCTGAACTTCTCCTATGGCAGCAACCTGTG
GACTGAGAGGATCCACCTACGAAACCCATTGGTTACGTTCTGCAGTGTGGCCTGCCTGCAAGATTTTAAGCTTGACTTTG
GCAATTCCCAAGGCAAAATAAGTGATACCTGGCATGAAGGAATAGTTACCATATTTCAAAGTCCTGGAGATGAAGTGTGG
GGAGTAGTTTGGAAAATGAATGAAAGCAGTTAAGTTCTCTGGATAAGCAAGAAGGGGTTATAAGTGGAACATATGATTCA
ATAGAAGTAATTGTTCATGCTCAAGAAGGAAATGAACTAACTTGTCAAAGTTAGCAGATGAAAACTTGTGTGATTCCTCC
CCCATCACCACAATTTAAAAAAGTCATTTGCATGACTGCAAAAGAAAATGGTTTACTCCCGGAGTATCAAAAGAAGTTAA
AAGCAATAGAATAAAATGACTATAAAGGAAAGGTCTCAGAAGAAATTGAAAATATTATCAAAAAGGGGAAATAAAAACTC
AGG

Alignment

ORF - retro_dnov_2324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADSGCRSCQGRDEESFLYFTYASNLLTERIHLQNPSATFCCVACLQDFKLDFGNSEGKISDTWHGGIAT
          M...GCR.CQGRD.E.FL.F.Y.SNL.TERIHL.NP..TFC.VACLQDFKLDFGNS.GKISDTWH.GI.T
Retrocopy MVGLGCRNCQGRDKENFLNFSYGSNLWTERIHLRNPLVTFCSVACLQDFKLDFGNSQGKISDTWHEGIVT

Parental  IFQSPGDEVWGVIWKMNKSN-LSSLDVQEGVVSGTYDPIEVTVHTREGKEITCRSYQMKNYVSVPPSPQY
          IFQSPGDEVWGV.WKMN.S..LSSLD.QEGV.SGTYD.IEV.VH..EG.E.TC.S.QMK..V..PPSPQ.
Retrocopy IFQSPGDEVWGVVWKMNESS<LSSLDKQEGVISGTYDSIEVIVHAQEGNELTCQS*QMKTCVIPPPSPQF

Parental  KKVICMGAEENGLPLEYQKKLKAIEPNDYKGKVSEEIEDIIKKGEVKLQ
          KKVICM.A.ENGL..EYQKKLKAIE.NDYKGKVSEEIE.IIKKG..KL.
Retrocopy KKVICMTAKENGLLPEYQKKLKAIE*NDYKGKVSEEIENIIKKGK*KLR

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	11.67 RPM
SRP012922_cerebellum	0.00 RPM	1.65 RPM
SRP012922_heart	0.00 RPM	2.55 RPM
SRP012922_kidney	0.00 RPM	13.96 RPM
SRP012922_liver	0.15 RPM	4.49 RPM
SRP012922_lung	0.46 RPM	10.23 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.56 RPM
SRP012922_spleen	0.69 RPM	13.62 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_2324 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008757	1 retrocopy	retro_chof_467,
Callithrix jacchus	ENSCJAG00000008589	1 retrocopy	retro_cjac_1211,
Dasypus novemcinctus	ENSDNOG00000007242	1 retrocopy	retro_dnov_2324 ,
Mustela putorius furo	ENSMPUG00000005083	1 retrocopy	retro_mputfur_1157,
Otolemur garnettii	ENSOGAG00000013316	1 retrocopy	retro_ogar_2457,
Ochotona princeps	ENSOPRG00000005329	2 retrocopies	retro_opri_170, retro_opri_505,