RetrogeneDB ID: retro_dnov_1602

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_245662:2..467(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000008497
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MLF2
• Ensembl ID: ENSDNOG00000000758
• Aliases: None
• Description: myeloid leukemia factor 2 [Source:HGNC Symbol;Acc:7126]

Sequence

>retro_dnov_1602
ATGACAGCTGGAGGCAATTGCCAGACCTTTTACTTAAGAGTGCCCTCTCCTACTCCAATACGGGGGATGGTGGCCTAAAG
TCTACCAGGAGACATCAGAGATGCGCTCAGCACCAGGAGGGATCCGGGAGACACGGAGGACTGTACGGGACTCAGACAGT
GGCCTAGAGCAGATGTCCATTGGGCATCACATCCGAGACAGGGCTCACATCCTGCAGCGCTCCCGAAACCACCGTACAGG
GGACCAGGAGGAGCGGCAGGACTACCTCAACCTGGATGAGAGTGAGGCTGCAGCATTTGATGATGAGTGGCGGAGGGAGA
CTTCCCAATTCCAGCAGCAGCGCCCTCTGGAATTTCAACGGCATGAGGCTTCAGGGGGTGGGGGCCGAAGGGCTGAGGGG
CCTCCCCGCCTGGCTATACAGGGACCTGAGGACTCCCCTCCCGACAGTCCCGCCGCTATGACTGG

Alignment

ORF - retro_dnov_1602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.31 %
• Parental protein coverage: 79.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTAGGNCQTFSS-STVISYSNTGDGA-PKVYQETSEMRSAPGGIRETRRTVRDSDSGLEQMSIGHHIRDR
          MTAGGNCQTF.......SYSNTGDG..PKVYQETSEMRSAPGGIRETRRTVRDSDSGLEQMSIGHHIRDR
Retrocopy MTAGGNCQTFYL<KSALSYSNTGDGG<PKVYQETSEMRSAPGGIRETRRTVRDSDSGLEQMSIGHHIRDR

Parental  AHILQRSRNHRTGDQEERQDYINLD--EAAAFDDEWQRETSRFRQQRPLEFRRHEASGGGGRRAEGPPRL
          AHILQRSRNHRTGDQEERQDY.NLD..EAAAFDDEW.RETS.F.QQRPLEF.RHEASGGGGRRAEGPPRL
Retrocopy AHILQRSRNHRTGDQEERQDYLNLDESEAAAFDDEWRRETSQFQQQRPLEFQRHEASGGGGRRAEGPPRL

Parental  AIQGPEDS-PSRQSRRYDW
          AIQGPEDS.PSRQSRRYDW
Retrocopy AIQGPEDS<PSRQSRRYDW

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	29.56 RPM
SRP012922_cerebellum	0.00 RPM	104.34 RPM
SRP012922_heart	0.23 RPM	17.63 RPM
SRP012922_kidney	0.27 RPM	56.68 RPM
SRP012922_liver	0.15 RPM	27.71 RPM
SRP012922_lung	0.00 RPM	27.34 RPM
SRP012922_quadricep_muscle	0.17 RPM	13.33 RPM
SRP012922_spleen	0.46 RPM	30.90 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_1602 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000758	2 retrocopies	retro_dnov_1602 , retro_dnov_649,
Echinops telfairi	ENSETEG00000014471	2 retrocopies	retro_etel_1236, retro_etel_233,
Microcebus murinus	ENSMICG00000010652	1 retrocopy	retro_mmur_449,
Monodelphis domestica	ENSMODG00000018113	1 retrocopy	retro_mdom_324,
Mus musculus	ENSMUSG00000030120	1 retrocopy	retro_mmus_1090,
Otolemur garnettii	ENSOGAG00000005976	1 retrocopy	retro_ogar_232,
Procavia capensis	ENSPCAG00000001026	1 retrocopy	retro_pcap_326,
Ictidomys tridecemlineatus	ENSSTOG00000009908	1 retrocopy	retro_itri_1707,