RetrogeneDB ID: retro_dnov_1680

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_265102:187..1033(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK38L
• Ensembl ID: ENSDNOG00000025573
• Aliases: None
• Description: serine/threonine kinase 38 like [Source:HGNC Symbol;Acc:17848]

Sequence

>retro_dnov_1680
GTGGCCCATATTCGAGCAGAAAGAGATATTTTGGTTGAAGCAGATGGTGCCTGGGTGGTGAAGATGTTTTACAGTTTTCA
GGATAAGAGGAACCTCTATCTAATCATGGAATTTCTCCCTGGAGGTGACATGATGACACTGTTAATGAAGAAAGACACCT
TGACAGAAGAAGAAACCCAGTTCTACATTTCAGAGACGGTTCTGGCAATAGATGCAATCCATCAATTGGGTTTCATCCAT
CGAGATATTAAACCAGACAACCTTTTACTGGATGCCAAGGGTCATGTAAAATTGTCTGATTTTGGTTTATGCACGGGATT
AAAGAAAGCTCACAGGACTGAATTCTACCGAAACCTCACCCACAACCCACCAAGCGACTTCTCATTTCAGAACATGAACT
CGAAGAGGAAGGCTGAGACCTGGAAGAAGAACAGGAGGCAGCTGGCATACTCAACTGTCGGCACACCGGATTACATCGCC
CCGGAAGTGTTCATGCAGACGGGCTACAACAAACTGTGCGACTGGTGGTCTCTGGGAGTGATCATGTATGAGATGCTAAT
AGGGTACCCACCTTTCTGCTCGGAAACGCCTCAAGAGACGTACAGAAAAGTGATGAGCTGGAAAGAAACGCTGGTATTCT
CTCCAGAGGTGCTCGATAGCTGAGAAAGCTAAAGCCTTAATTCTCAGATTTTGTATTGATTCTGAAAATAGAATTGGAAA
TAGTGGAGTAGAAGAAATAAAAGGTCATCTCTTCTTTGAAGGTGTAGACTGGGGGTCACATCAGGGAAAGGTCAGCAGCC
AATCTCTATAGAAATCTAAAGCATTGATGACACTTCAAATTTCGAT

Alignment

ORF - retro_dnov_1680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.48 %
• Parental protein coverage: 60.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VAHIRAERDILVEADGAWVVKMFYSFQAKRNQYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAI
          VAHIRAERDILVEADGAWVVKMFYSFQ.KRN.YLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAI
Retrocopy VAHIRAERDILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAI

Parental  DAIHQLGFIHRDIKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAET
          DAIHQLGFIHRDIKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAET
Retrocopy DAIHQLGFIHRDIKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAET

Parental  WKKNRRQLAYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGYPPFCSETPQETYRKVMSWKET
          WKKNRRQLAYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGYPPFCSETPQETYRKVMSWKET
Retrocopy WKKNRRQLAYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGYPPFCSETPQETYRKVMSWKET

Parental  LVFSPEV-PIAEKAKALILRFCIDSENRIGNSGVEEIKGHPFFEGVDW-GHIRERPAA-IPIEIKSIDDT
          LVFSPEV..IAEKAKALILRFCIDSENRIGNSGVEEIKGH.FFEGVDW.GHIRER.AA.I.IEI.SIDDT
Retrocopy LVFSPEV>SIAEKAKALILRFCIDSENRIGNSGVEEIKGHLFFEGVDW>GHIRERSAA>ISIEI*SIDDT

Parental  SNFD
          SNFD
Retrocopy SNFD

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	5.45 RPM	25.67 RPM
SRP012922_cerebellum	1.65 RPM	11.82 RPM
SRP012922_heart	1.16 RPM	6.03 RPM
SRP012922_kidney	0.55 RPM	10.68 RPM
SRP012922_liver	3.25 RPM	24.30 RPM
SRP012922_lung	1.37 RPM	18.48 RPM
SRP012922_quadricep_muscle	2.77 RPM	15.40 RPM
SRP012922_spleen	2.52 RPM	19.80 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_1680 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000025573	1 retrocopy	retro_dnov_1680 ,
Monodelphis domestica	ENSMODG00000016636	1 retrocopy	retro_mdom_1913,
Mus musculus	ENSMUSG00000001630	2 retrocopies	retro_mmus_3100, retro_mmus_347,