RetrogeneDB ID: retro_dnov_1537

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_22972:19403..19929(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAX1
• Ensembl ID: ENSDNOG00000016727
• Aliases: None
• Description: HCLS1 associated protein X-1 [Source:HGNC Symbol;Acc:16915]

Sequence

>retro_dnov_1537
AGCCCCAGGTTTGGGGTTCCTCAGCCCTCTGAGGAATTGGGCTTCAGCTTCAATCCAGGAGGAAGGATAATTTTCCATGA
TAACTTCGGCTTTGGTGACCTCTTAGGGGATTTCAATAACTTCTTCAGTGAAATGGGAGGCTGGACGTTACCTTCCCGTT
CTCCTGAACCTCCAGGTCCTGAGTCAGAGACACATGGTGAGAGACAGAGGGAGGGAGAGATGCTTCGAGACTCAATACTT
AAGTGTCCAGATAGTCACCAGTCCAGACTTTGGGAGGGGGAGGTTTCCTAGGAGAGTTATGCAGGAACAGAATCCTCTAA
ATCAGCACCAGATTGGGGTTCCCAGAGACCTTTTCATAGGTTTGATGATATGTGGTCTGTGATGTCCCAGAGAGGACAAT
GATCTTGACTCTCAGCTTTCCCAGGAAAGTCTTAGACCAGTTCTGCAACCCCAGCCCAAATCCTATTTCAAGAGCATTTC
TGTGACCAAGATCACTAAGCCAGATGGATTAGTGGAGGAGCACAGA

Alignment

ORF - retro_dnov_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.89 %
• Parental protein coverage: 63.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPRFGVPQHPEEFGFSFSPGGGIHFHDNFGFDDLVRDFNNIFSEMGAWTLPSHS-DLPGPESETPGERWR
          SPRFGVPQ..EE.GFSF.PGG.I.FHDNFGF.DL..DFNN.FSEMG.WTLPS.S...PGPESET.GER.R
Retrocopy SPRFGVPQPSEELGFSFNPGGRIIFHDNFGFGDLLGDFNNFFSEMGGWTLPSRSPEPPGPESETHGERQR

Parental  EGETLRDSMLKYPDSHQPRIFGGVL--ESDAGTESPKSAPDWGSQRPFHRFDDMWPV-TPHPRTREDNDL
          EGE.LRDS.LK.PDSHQ.R...G....ES.AGTES.KSAPDWGSQRPFHRFDDMW.V..P......D..L
Retrocopy EGEMLRDSILKCPDSHQSRLWEGEVS*ESYAGTESSKSAPDWGSQRPFHRFDDMWSV>CPREDNDLDSQL

Parental  DSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGTVEERR
          ........L.P..QP..KSYFKSISVTKITKPDG.VEE.R
Retrocopy SQESLRPVLQP--QP--KSYFKSISVTKITKPDGLVEEHR

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	63.01 RPM
SRP012922_cerebellum	0.00 RPM	57.87 RPM
SRP012922_heart	0.00 RPM	95.36 RPM
SRP012922_kidney	0.00 RPM	85.70 RPM
SRP012922_liver	0.00 RPM	71.06 RPM
SRP012922_lung	0.00 RPM	76.67 RPM
SRP012922_quadricep_muscle	0.00 RPM	105.58 RPM
SRP012922_spleen	0.00 RPM	71.65 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_1537 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537 ,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,