RetrogeneDB ID: retro_dnov_58

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1137:256589..257138(+)
• Located in intron of: ENSDNOG00000015876

Retrocopy information

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

Parental gene information

• Parental gene symbol: HESX1
• Ensembl ID: ENSDNOG00000003677
• Aliases: None
• Description: HESX homeobox 1 [Source:HGNC Symbol;Acc:4877]

Sequence

>retro_dnov_58
ATGTCCCCCGGCCTTCAGGAAGACGTTTGGCTCAGGGAAAGCAGACCTCACTCTGCTCCTTTGCAGCTGAAAGCCTCTTA
GGGCTGGGCCAGAAGAGAGACTGTGGTCTGTCGGTGAAGCCCCACGGGCCCTAGGCAGACCCTGCGGCTCCTCGGGCGTG
ATGGAAACCTGTGCCCACAGGTCTCCAGCCTTCCCGATGGCATCTCCTTCCTTTGTTTCATGGGCCATCGAGGGCAAGAA
GAAAGAGTTCCGAAACATGAAAATTACTTTTCACCTTCGGAAAGACTGTCTTTGAAGAGAGTTGGGTTTGTTTAGAGGCC
AAAGACTAAGAATTGCTTTTTCTCAAAACCAGATGAAATTTTGGAAAATGTCTTTAGAGTAAACTAGCTATTCTGGCATC
GAGGTCCGAGAAGACTTAGCTCGAAAACTGAATCGAGACAAAGACCAAATCCAAACCTGTTCCAAAATCAGCATACAAAG
CTGAAAAGGTCCTTCAGAGAATCACAGTTCCTAATGGTGAAAAAATATTTCACACATCCCCTGAAAGAG

Alignment

ORF - retro_dnov_58 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSPSLQDGSRLGESKP-SPCSFSIESILGLDQKQDCRPSEKPHRPWADT-CRSSG-KDGNLCLHVPSLPN
          MSP.LQ....L.ES.P.S.CSF..ES.LGL.QK.DC..S.KPH.P.AD..C.SSG..DGNLC..V.SLP.
Retrocopy MSPGLQEDVWLRESRP<SLCSFAAESLLGLGQKRDCGLSVKPHGP*ADP<CGSSG<RDGNLCPQVSSLPD

Parental  GISFSCTVDHPVPEETVLKYENYFSPSQRLSLKRELSWYRGRRPRTAFTQNQIEVLEDVFRVN-CYPGID
          GISF.C...H...EE.V.K.ENYFSPS.RLSLKR.............F.....E.LE.VFRVN..Y.GI.
Retrocopy GISFLCFMGHRGQEERVPKHENYFSPSERLSLKR-VGFV*RPKTKNCFFSKPDEILENVFRVN>SYSGIE

Parental  IREELAQKLNLEEDRIQI-WFQNRRAKLKRSHKESQFLMAKKNFDTNLLE
          .RE.LA.KLN...D.IQ...FQN...KLKRS..ESQFLM.KK.F...L.E
Retrocopy VREDLARKLNRDKDQIQT<LFQNQHTKLKRSFRESQFLMVKKYFTHPLKE

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	0.00 RPM
SRP012922_cerebellum	0.27 RPM	0.00 RPM
SRP012922_heart	0.70 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.15 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.00 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_58 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
Ailuropoda melanoleuca	ENSAMEG00000011722	1 retrocopy	retro_amel_862,
Choloepus hoffmanni	ENSCHOG00000013897	1 retrocopy	retro_chof_123,
Callithrix jacchus	ENSCJAG00000010981	1 retrocopy	retro_cjac_891,
Cavia porcellus	ENSCPOG00000012741	1 retrocopy	retro_cpor_1067,
Dasypus novemcinctus	ENSDNOG00000003677	1 retrocopy	retro_dnov_58 ,
Mustela putorius furo	ENSMPUG00000016854	2 retrocopies	retro_mputfur_112, retro_mputfur_174,