RetrogeneDB ID: retro_dnov_440

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4730:322309..323188(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000018579
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM237
• Ensembl ID: ENSDNOG00000002126
• Aliases: None
• Description: transmembrane protein 237 [Source:HGNC Symbol;Acc:14432]

Sequence

>retro_dnov_440
TTGGAGACTTCCTTCACCCAAAAGATATCTAGTCCATTTTTATTACGAAATGAAAATGGTATTGATGGGGAGCCAGCTGA
AGAGGCAGTTTCTCAAAAACCTCGAAAGAAGAAAAAGAAAACTCAGCCAGCAGAATTACAGTATGCAAATGAGCTAGGAG
TAGAAGATGAAGACATAATTACTGATGAGCAAAGTGGTCCAGAGCAACAGTCTGTATTCACTGCACCCACTGGCGTTAGC
CAGCCTGTAGGCAAAGTATTTGTGGAAAAAAGCCGCCGATTCCAGGCCGCTGATCGTTCAGAGTTGATAAAGACCACAGA
AAATGTAGATGTGTCCATGGACCTGAAGCCTTCCTGGACGACCAGAGATGTTGCACTTTCAGTACACCGGGCTTTCAGGA
TGATTGGTCTCTTTTCTCATGGCTTCTTGGCTGGCTGCGCTGTGTGGAATATTGTTGTGATATATGTTCTAGCAGGAGAT
CAACTATCTAATCTCTCAAACCTTCTGCAGCAATATAAGACTTTAGCATATCCATTCCAGAGTCTTCTCTACATGCTTTT
GGCTCTAAGTACAATTTCAGCTTTTGACAGGATTGACTTGGCTAAAACATCAGTAGCCATCCGAAGTTTTCTTGCCCTGG
ATCCAACAGCTTTAGCATCTTTTTTGTACTTTGCTGCTCTTATACTATCCTTGAGTCAACAAGTGACAAGTGACAGAATC
CACCTTTACACACCTCCTTCTGTTAATGGTAGCCTCTGGGCAACAGGAAATGAGGAACAGATTCTCCAACCATGGATTGT
GGTGAATCTAGTGGTGGCCCTGCTGGTTGGATTATCTTGGGTTTTTTTGTCTTATAGACCAGGCGTGGATCTTAGTGAA

Alignment

ORF - retro_dnov_440 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.66 %
• Parental protein coverage: 75.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LETSFTQKISSPFLLRNENGIDGEPAEEAVSQKPRKKKKKTQPAELQYANELGVEDEDIITNEQSGPEQQ
          LETSFTQKISSPFLLRNENGIDGEPAEEAVSQKPRKKKKKTQPAELQYANELGVEDEDIIT.EQSGPEQQ
Retrocopy LETSFTQKISSPFLLRNENGIDGEPAEEAVSQKPRKKKKKTQPAELQYANELGVEDEDIITDEQSGPEQQ

Parental  SVFTAPTGVSQPVGKVFVEKSRRFQAADRSELIKTTENVDVSMDLKPSWTTRDVALSVHRAFRMIGLFSH
          SVFTAPTGVSQPVGKVFVEKSRRFQAADRSELIKTTENVDVSMDLKPSWTTRDVALSVHRAFRMIGLFSH
Retrocopy SVFTAPTGVSQPVGKVFVEKSRRFQAADRSELIKTTENVDVSMDLKPSWTTRDVALSVHRAFRMIGLFSH

Parental  GFLAGCAVWNIVVIYVLAGDQLSNLSNLLQQYKTLAYPFQSLLYMLLALSTISAFDRIDLAKTSVAIRSF
          GFLAGCAVWNIVVIYVLAGDQLSNLSNLLQQYKTLAYPFQSLLYMLLALSTISAFDRIDLAKTSVAIRSF
Retrocopy GFLAGCAVWNIVVIYVLAGDQLSNLSNLLQQYKTLAYPFQSLLYMLLALSTISAFDRIDLAKTSVAIRSF

Parental  LALDPTALASFLYFAALILSLSQQVTSDRIHLYTPPSVNGSLWATGNEEQILQPWIVVNLVVALLVGLSW
          LALDPTALASFLYFAALILSLSQQVTSDRIHLYTPPSVNGSLWATGNEEQILQPWIVVNLVVALLVGLSW
Retrocopy LALDPTALASFLYFAALILSLSQQVTSDRIHLYTPPSVNGSLWATGNEEQILQPWIVVNLVVALLVGLSW

Parental  VFLSYRPGVDLSE
          VFLSYRPGVDLSE
Retrocopy VFLSYRPGVDLSE

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	0.58 RPM	0.39 RPM
SRP012922_cerebellum	4.67 RPM	4.26 RPM
SRP012922_heart	2.32 RPM	1.86 RPM
SRP012922_kidney	2.74 RPM	2.74 RPM
SRP012922_liver	0.93 RPM	0.15 RPM
SRP012922_lung	5.80 RPM	3.05 RPM
SRP012922_quadricep_muscle	1.56 RPM	0.35 RPM
SRP012922_spleen	2.98 RPM	2.98 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_440 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002126	1 retrocopy	retro_dnov_440 ,
Echinops telfairi	ENSETEG00000003826	1 retrocopy	retro_etel_17,
Tupaia belangeri	ENSTBEG00000009845	1 retrocopy	retro_tbel_3487,