RetrogeneDB ID: retro_dnov_2425

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_7390:27326..28129(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK8
• Ensembl ID: ENSDNOG00000008538
• Aliases: None
• Description: mitogen-activated protein kinase 8 [Source:HGNC Symbol;Acc:6881]

Sequence

>retro_dnov_2425
ACTCGTGCAAAGAGAACTTGCCATGAACTTGTCCTCTTAAAATGTGTCAATCATAAAATCATAGTTTGTTAAAGGTATTT
ATATCACAAAGAACTCTAGAAGATCTTCAAGATGTGTATTTGGCTATGGAATTAATGGATGCTAACTTATGTCAGGTTAC
GCATTTGGACTGGAAACAGTAAAGAATGTCCTATCTTCTTTACCAGATGTTTTGTGGTATTAAACATGTGCATTCCGCTG
GTATAATTCATAGAGATTTGTAACCTACCAAATTCGTGATATAGTCAGCCTGCACCCTTAAGATCCTCGACTTTTGCTTG
GCCGGGACAGCTGGCACCAACATTATGATGACCCCTACATGGTGACATGGTATCTTCAAGGCCCTGAAGTCATTCTTGGG
ATGGGGTACAAAGAGAATGTTCATATTGATATTCGTTTAGTGGATTACATTATGGAGACCTGGTGAAAGGTTCTGTGATA
TTCCAAGTCACTGACCATATTGATCAGTGGAGTCAAGTTATTGAGCAGCTGGGAACACCATCAGCAGATTTTATGGAGAA
ACTTCAGCCAACTGTGAGGAATTATGTAGAAAACCAACATAGTATCTAGGCATCAAATGTGAAGAACTCTTTCCAGACTG
GATATTTCCTTTAGAGTCTGAGTGAGAAAAAATGTAAACAAGTCAAACCAGAGATCTGTTATTGAAAATGTTAGTGAACG
CTCCCGACAAGAGGATCTCTGTAGATGAAGTTTTGCACAGCCAGTATTTAACTGTTTGGTGTGACCCTGATGAAGCAGAA
GCA

Alignment

ORF - retro_dnov_2425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.77 %
• Parental protein coverage: 62.91 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  THAKRAYRELVLMKCVNHKNII-GLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLY
          T.AKR...ELVL.KCVNHK.II..LL.VF..Q..LE..QDVY..MELMDANLCQV........RMSYLLY
Retrocopy TRAKRTCHELVLLKCVNHK-II<SLLKVFISQRTLEDLQDVYLAMELMDANLCQVTHLDWKQ*RMSYLLY

Parental  QMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMT-PYVVTRYYRAPEVILGMGY
          QM.CGIKH.HSAGIIHRDL.P...V..S.CTLKILDF.LA.TAGT..MMT.PY.VT.Y...PEVILGMGY
Retrocopy QMFCGIKHVHSAGIIHRDL*PTKFVI*SACTLKILDFCLAGTAGTNIMMT<PYMVTWYLQGPEVILGMGY

Parental  KENV--DLWSVGCIM-GEMVCHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPK-YAG
          KENV..D...V..IM.G..V.....F...D.IDQW..VIEQLGTP...FM.KLQPTVR.YVEN....Y.G
Retrocopy KENVHIDIRLVDYIM<GDLVKGSVIFQVTDHIDQWSQVIEQLGTPSADFMEKLQPTVRNYVENQHS<YLG

Parental  YSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDASKRISVDEALQHPYINVWYDPSEAEA
          ...E.LFPD..FP..SE..K...SQ.RDLL.KMLV....KRISVDE.L...Y..VW.DP.EAEA
Retrocopy IKCEELFPDWIFPLESE*EKM*TSQTRDLLLKMLVNAPDKRISVDEVLHSQYLTVWCDPDEAEA

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	19.45 RPM
SRP012922_cerebellum	0.00 RPM	26.26 RPM
SRP012922_heart	0.00 RPM	5.80 RPM
SRP012922_kidney	0.27 RPM	24.37 RPM
SRP012922_liver	0.00 RPM	8.67 RPM
SRP012922_lung	0.00 RPM	11.61 RPM
SRP012922_quadricep_muscle	0.00 RPM	14.37 RPM
SRP012922_spleen	0.00 RPM	11.56 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_2425 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000009313	1 retrocopy	retro_cint_23,
Ciona savignyi	ENSCSAVG00000005955	1 retrocopy	retro_csav_12,
Dasypus novemcinctus	ENSDNOG00000008538	1 retrocopy	retro_dnov_2425 ,
Myotis lucifugus	ENSMLUG00000014533	1 retrocopy	retro_mluc_888,