RetrogeneDB ID: retro_dnov_251

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3025:38778..39413(+)
• Located in intron of: ENSDNOG00000019564

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARG2
• Ensembl ID: ENSDNOG00000004808
• Aliases: None
• Description: arginase 2 [Source:HGNC Symbol;Acc:664]

Sequence

>retro_dnov_251
CCAGTCCCCAAAGATGATCTCTATAATAATGTAATAGTGAATCCTCCCTCAGTGGGCCTTGTCAATCAGGAACTGGCCAG
GGTGGTTAGTAGAGCTGTGTCAAGTGGCTACAGCTACATTACAGTAGGAGAATACCAGTCTGGCCATGGGTACCATTAGT
GGCCACACCCAGCACTGCCCCAACCTCTGGGGCATCTGGATTGATGCACACGCTGACATCAATACACCCCTTACCACTTT
ATCTGGAAATCTCCATGGACAGCCAGTTTCATTTCTCCTCAGAGAACTACAGGATAAAGTACCACAACCCCAAGGTTTTT
CCTGGATCAAACCTTTTATCTCTTTTCCAGATACCGTGTATATTGGTTTAAGTGATGTGGACCCGCCTGATCATTATATT
TTAAAGAACTATGATATCCAATATTTTTCCATGAGGGATATTGATCGACTTGGTATTCAAAAGGTCATGGAACAGACATT
TGATCTGCTGATTGGCAAAAGACAAAGGCCAATCCACCTGAGTTTTGAAACTGATGCATTTGGCCCTACGAAAGCTCCAG
CCACAGGTACCCCTGTTGTAGGGGGACTGACCTACCGAGAAGGCATGTATTATTACTGAGGAAATACACAATACA

Alignment

ORF - retro_dnov_251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.58 %
• Parental protein coverage: 74.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVPKDDLYNNLIVNPRSVGLANQELAEVVSRAVSSGYRCVTVGGDH-SLAIGTISGHTRHCPNLCVIWID
          PVPKDDLYNN.IVNP.SVGL.NQELA.VVSRAVSSGY...TV.G...SLA.GTISGHT.HCPNL..IWID
Retrocopy PVPKDDLYNNVIVNPPSVGLVNQELARVVSRAVSSGYSYITV-GEY>SLAMGTISGHTQHCPNLWGIWID

Parental  AHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWIKPCISSPDIVYIGLRDVDPPEHYILKNYD
          AHADINTPLTT.SGNLHGQPVSFLLRELQDKVPQ..GFSWIKP.IS.PD.VYIGL.DVDPP.HYILKNYD
Retrocopy AHADINTPLTTLSGNLHGQPVSFLLRELQDKVPQPQGFSWIKPFISFPDTVYIGLSDVDPPDHYILKNYD

Parental  IQYFSMRDIDRLGIQKVMEQTFDLLIGKTQRPIHLSFDIDAFDPTLAPAT-TP-VGELTYREGMY-IT-E
          IQYFSMRDIDRLGIQKVMEQTFDLLIGK.QRPIHLSF..DAF.PT.APAT.TP.VG.LTYREGMY.IT.E
Retrocopy IQYFSMRDIDRLGIQKVMEQTFDLLIGKRQRPIHLSFETDAFGPTKAPATGTPVVGGLTYREGMY>ITEE

Parental  IHNT
          IHNT
Retrocopy IHNT

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	0.58 RPM	7.78 RPM
SRP012922_cerebellum	0.41 RPM	12.65 RPM
SRP012922_heart	0.70 RPM	2.32 RPM
SRP012922_kidney	1.37 RPM	16.15 RPM
SRP012922_liver	2.01 RPM	13.78 RPM
SRP012922_lung	1.37 RPM	9.32 RPM
SRP012922_quadricep_muscle	0.69 RPM	5.19 RPM
SRP012922_spleen	0.57 RPM	5.49 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_251 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357, retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251 ,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Microcebus murinus	ENSMICG00000010837	1 retrocopy	retro_mmur_874,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,