RetrogeneDB ID: retro_dnov_2395

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_71036:3588..4067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CUTA
• Ensembl ID: ENSDNOG00000009616
• Aliases: None
• Description: cutA divalent cation tolerance homolog (E. coli) [Source:HGNC Symbol;Acc:21101]

Sequence

>retro_dnov_2395
GCTGCTCTGCTCCTGGTGCTTCTTTGGATGACGGCACTGTTGCCTGTGATCTCCCACCTTCTATTACTACTGAGAACCCT
GCTCTCCATGGCCTCTGGAAACCCTCCCATCCCAGTTCCCACCAGTCTCGGGCTCTGCCTACATCTCTGGCTCAGAGCAG
CCTTTGTTACCTGCCCCAATGAGAAGGTGGCCAAAGATATCACCAGGCTGTGGTAGAAAAGCATCTGGCAGCCTGAGTCC
ACCTCATCCTGCAGATTATATCCATTTATAAGCAGAAAGGAAAGATTGGGAGGGAAGTGAGGTGTTGATGATGACTGAAA
CCCAAGTTCCTTGGTCCCAGTTTTGACAGATTTTGTTTGTTCTGTGCACCCTTATGAAGTGGCTGAGGTGATTGCATTGC
CTGTGGAGAGGGAAACTCCCCACACTTGCACTGGGTGTGCCAGGTCACAGGGTCAGTTTCTGACTCCAACTCAGCCCTG

Alignment

ORF - retro_dnov_2395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.29 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AALLLSLLWMPALLPVASRLLLLPRALLSMASGNPPPQSPPASGSAYVPGSVSAAFVTCPNEKVAKEIAR
          AALLL.LLWM.ALLPV.S.LLLL.R.LLSMASGNP.P...P.S..........AAFVTCPNEKVAK.I.R
Retrocopy AALLLVLLWMTALLPVISHLLLLLRTLLSMASGNP-PIPVPTSLGLCLHLWLRAAFVTCPNEKVAKDITR

Parental  -AVVEKRLAACVNLIPQITSIYEWKGKIE-EDSEVLMMIKTQ-SSLVPALTDFVRSVHPYEVAEVIALPV
          .AVVEK.LAA.V.LI.QI.SIY..KGKI..E.SEVLMM..TQ.SSLVP.LTDFV.SVHPYEVAEVIALPV
Retrocopy <AVVEKHLAA*VHLILQIISIYKQKGKIG<EGSEVLMMTETQ<SSLVPVLTDFVCSVHPYEVAEVIALPV

Parental  E-QGNSPYLHWVRQVTESVSDSSTAL
          E..GNSP.LHWV.QVT.SVSDS..AL
Retrocopy E<EGNSPHLHWVCQVTGSVSDSNSAL

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	50.95 RPM
SRP012922_cerebellum	0.00 RPM	47.15 RPM
SRP012922_heart	0.00 RPM	51.51 RPM
SRP012922_kidney	0.00 RPM	170.57 RPM
SRP012922_liver	0.00 RPM	47.53 RPM
SRP012922_lung	0.00 RPM	74.68 RPM
SRP012922_quadricep_muscle	0.00 RPM	45.52 RPM
SRP012922_spleen	0.00 RPM	64.33 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_2395 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009616	1 retrocopy	retro_dnov_2395 ,
Otolemur garnettii	ENSOGAG00000015556	1 retrocopy	retro_ogar_2719,
Ictidomys tridecemlineatus	ENSSTOG00000002474	1 retrocopy	retro_itri_904,