RetrogeneDB ID: retro_dnov_1286

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_176358:915..1193(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED10
• Ensembl ID: ENSDNOG00000004579
• Aliases: None
• Description: mediator complex subunit 10 [Source:HGNC Symbol;Acc:28760]

Sequence

>retro_dnov_1286
TTTATCATTACTGGCCTTAAGGACATTGATAAGTGCAGACAGCAGCTGCATGCTATCACTGCACCGTTAGAAGTTTTCGA
CTATGTAGATCAAAGTTGAAACCCCCAGGTCCACACCAAAGAGTGCCTGGAGAGGCTGCTAGCGAAAAATGAGCAAGTCA
AAGGCCAGATGGCAGGATGAAGAATTTTAAGAGCCTGTTGGCTCAAGAACTCTCGAAAGTATCTCCAGAGGACGAGGCGA
AGTGTGGCAGCCTCTGAGGCGAGCACCGCCCGCCATCC

Alignment

ORF - retro_dnov_1286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.34 %
• Parental protein coverage: 98.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FIVTGLQDIDKCRQQLHDITVPLEVFEYIDQGRNPQLYTKECLERALAKNEQVKGKI-DTMKKFKSLLIQ
          FI.TGL.DIDKCRQQLH.IT.PLEVF.Y.DQ..NPQ..TKECLER.LAKNEQVKG.....MK.FKSLL.Q
Retrocopy FIITGLKDIDKCRQQLHAITAPLEVFDYVDQS*NPQVHTKECLERLLAKNEQVKGQM<GRMKNFKSLLAQ

Parental  ELSKVFPEDMAKYRSIRGEDHPPS
          ELSKV.PED.AK..S..GE..PPS
Retrocopy ELSKVSPEDEAKCGSL*GEHRPPS

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	7.97 RPM
SRP012922_cerebellum	0.00 RPM	10.86 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	12.87 RPM
SRP012922_liver	0.00 RPM	3.56 RPM
SRP012922_lung	0.00 RPM	9.93 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.94 RPM
SRP012922_spleen	0.00 RPM	10.87 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_1286 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006767	1 retrocopy	retro_amel_1034,
Canis familiaris	ENSCAFG00000010346	1 retrocopy	retro_cfam_721,
Dasypus novemcinctus	ENSDNOG00000004579	1 retrocopy	retro_dnov_1286 ,
Equus caballus	ENSECAG00000023738	1 retrocopy	retro_ecab_796,
Echinops telfairi	ENSETEG00000000027	1 retrocopy	retro_etel_1758,
Monodelphis domestica	ENSMODG00000002025	1 retrocopy	retro_mdom_399,
Otolemur garnettii	ENSOGAG00000005988	1 retrocopy	retro_ogar_1830,
Ochotona princeps	ENSOPRG00000015506	1 retrocopy	retro_opri_834,
Tupaia belangeri	ENSTBEG00000014579	2 retrocopies	retro_tbel_1647, retro_tbel_4561,
Tarsius syrichta	ENSTSYG00000002763	1 retrocopy	retro_tsyr_792,