RetrogeneDB ID: retro_dnov_1342

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_18450:23503..23994(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED4
• Ensembl ID: ENSDNOG00000018064
• Aliases: None
• Description: mediator complex subunit 4 [Source:HGNC Symbol;Acc:17903]

Sequence

>retro_dnov_1342
ATGACCACCTCCTCGTGTTCAGAGAAGGAGTAGGAGCGGCCCGGAGGTGGCGGTGGAGCGGCCAGGGTAACAACACGCGA
GAACGGCTGCTGTAGGCGCTGGACGACCTGGAGGTCCTGTCGAGGGAACTTGTAGAAATGTTGGCAATTTCAAGAAACCA
AAAGATGCTGCAACCTGGAGAGGAAAACCAGATTCTGGAGTTGTTAATTCACAGAGATGGGGAATTTCAAGAACTAATGA
AATTGGCTCTTAATCGGGGAAAAATCCATCATGAAATGCAAGTTTTAGAAAAATAAATTGAAAAGAGAGATAGTGATATT
CAGTAACTACAGAAACAACTAAAGGAAGCAGAACAAATACTGGCAACAGCTGTTTACCAAGCAAAAGAAAAACTCGAATC
AATAGAAAACGTGAGAAAAGGTGCTATCTTCTCTGAAGAAATAACTATAAGTATGCACACAGGATTAGTGCAAGTAATGC
TGTGTGTGCCC

Alignment

ORF - retro_dnov_1342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 60.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASSGSEKERERPGGGGGAAG-GNSTRERLLSALDDLEVLSRELIEMLAISRNQKMLQPGEENQILELL
          M..SS.SEKE.ERPGGGGGAA..GN.TRERLL.ALDDLEVLSREL.EMLAISRNQKMLQPGEENQILELL
Retrocopy MTTSSCSEKE*ERPGGGGGAAR<GNNTRERLL*ALDDLEVLSRELVEMLAISRNQKMLQPGEENQILELL

Parental  IHRDGEFQELMKLAVNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKAR
          IHRDGEFQELMKLA.N.GKIHHEMQVLEK..EKRDSDIQ.LQKQLKEAEQILATAVYQAKEKL.SIE..R
Retrocopy IHRDGEFQELMKLALNRGKIHHEMQVLEK*IEKRDSDIQ*LQKQLKEAEQILATAVYQAKEKLESIENVR

Parental  K-AISSEEIIKYAHRISASNAVCAP
          K.AI.SEEI....H........C.P
Retrocopy KGAIFSEEITISMHTGLVQVMLCVP

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	1.94 RPM	33.45 RPM
SRP012922_cerebellum	1.79 RPM	28.32 RPM
SRP012922_heart	0.70 RPM	16.47 RPM
SRP012922_kidney	1.92 RPM	27.38 RPM
SRP012922_liver	1.24 RPM	19.66 RPM
SRP012922_lung	0.92 RPM	29.93 RPM
SRP012922_quadricep_muscle	1.38 RPM	20.42 RPM
SRP012922_spleen	0.69 RPM	26.67 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_1342 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003718	1 retrocopy	retro_amel_1882,
Canis familiaris	ENSCAFG00000004451	1 retrocopy	retro_cfam_1792,
Callithrix jacchus	ENSCJAG00000009256	1 retrocopy	retro_cjac_3937,
Dasypus novemcinctus	ENSDNOG00000018064	1 retrocopy	retro_dnov_1342 ,
Myotis lucifugus	ENSMLUG00000009265	1 retrocopy	retro_mluc_178,
Mustela putorius furo	ENSMPUG00000001437	1 retrocopy	retro_mputfur_162,
Mus musculus	ENSMUSG00000022109	1 retrocopy	retro_mmus_3576,
Sorex araneus	ENSSARG00000001473	1 retrocopy	retro_sara_353,
Tupaia belangeri	ENSTBEG00000014259	1 retrocopy	retro_tbel_292,