RetrogeneDB ID: retro_dnov_1589

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_24116:11215..12798(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000005634
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SKIL
• Ensembl ID: ENSDNOG00000008923
• Aliases: None
• Description: SKI-like oncogene [Source:HGNC Symbol;Acc:10897]

Sequence

>retro_dnov_1589
ATGGAAAGCCTACAGACAAATTTTTCCTTGGTTCAGGGCTCAAATAAAAAACTGCATGGGATGGGAGATGAAGGCAGCCC
TCCAGTGAAAAAAATGATGACAGACATTCATGCAAATGGAAAAATGATGATACACAAGATGCCAACAGTAAAGAAGGAAC
ACTTGGAAGACTATGGAGAAGCACCAATGGAAACGGATGGAGAGCATGTCAAGCGAAACTGTGCCTCTGTGCCTGAACCT
TTAAATTTAAATCCCAGTTTGAAACATACATTGGCACAATTTCATTTAAGTAGTCAGAGCTCTCTGGGTGGGCCAGCAGC
ATTTTCTGCACGATATTCTCAAGAAAGCATGTCACCTACTGTATTTCTGCCCCTTCCATTCTCCTCAGGTTCTTCCTGGC
CCCCTCCTCATCCCTTCTGATAGCTCCACAGAACTCACCCAGACCGTGTTGGAGGGGGAGTCTATTTCATGTTTTCAGGT
TGGAGGAGAGAAGAGACTCTGTTTGCCCCAAGTCTTAAATTCTGTGCTCCGAGAATTTTCACTCCAGCAAATAAATACTG
TGTGTGATGAATTGTACATATATTGCTCAAGGTGCACTTCAGACCAGTTTCATATTTTAAAAGTCCTGGGAATTCTTCCG
TTCAATGCCCCATCCTGTGGGCTGATCACATTAACTGATGCACAAAGACTATGTAACGCTTTATTGCGACCACGCACTTT
TCCTCAAAATGGTAGCATGCTTTCTGCTAAAAACTCATTGGCCCAGCTAAAGGAAACTGGCAGTGCCTTTGAAGTGGAAC
ACGAATGCTTGGGCAAATGTCAGGGTCTGTTTGCACTGCAGTTTTATGTTCAGCCTGATGCTCCGTGTATTCAGTGTCTG
GAGAGCTGTGGAATGTTTGCACCCCAGACATTTGTGATGCATTCCCACAGATCACCTGACAAAAGGACTTGCCACTGGGG
CTTTGAATCTGCCAAATGGCATTGCTATCTTCATGTGAACCAAAAATACTTAGGGATACTTGAAGAAAAGAAACTGAAGA
TAGTTTTAGAAGAAATGAAGGAGAAATTTAGCATGAGAAATGGAAAAAGAACTCAGTCCAAGACAGATACACCATCAGGA
ATGGAATTACAGTCATGGTATCCTGTTATAAAGCAGGAAGGTGACCATGTTTCTCAGGCACATTCATTTTTACACCCCAG
CTACTGCTTATATATGTGTGATAAAGTAGTTGCACCCAATGTGTCTCTTACGTCTGCTGTATCCTAGGGTAAAGAGGTCA
CAAAGACAGAGGCAAGTAGGTCCATACTGAGACTGTCAGAGAAGCCTCACAGTAGTGGCAAACATCAAAAAATGGTGTCT
TATCCAGATGTCTCACTCGAAGAACAAGAGAAAATGGATTTAAAAACAAGTAGAGAATTATGTAGCCGTTCAGATTCATC
AATCTCAAATAATTCTGCAAGTAAAAAGAAATCTGAGTCTACTACTTGCAACTTTAAAACTAGAGACACAACCGAGATGG
AAACTGGGCCATGTTGCTGCAGCTTTATCTCCACTTCTTGTCAAAGATGTTACTTGTGTGGAT

Alignment

ORF - retro_dnov_1589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.22 %
• Parental protein coverage: 76.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MESLQTNFSLVQGSNKKLHGMGDEGSPPVKKMMTDIHANGKMMIHKMPTVKKEHLEDYGEAPMETDGDHV
          MESLQTNFSLVQGSNKKLHGMGDEGSPPVKKMMTDIHANGKMMIHKMPTVKKEHLEDYGEAPMETDG.HV
Retrocopy MESLQTNFSLVQGSNKKLHGMGDEGSPPVKKMMTDIHANGKMMIHKMPTVKKEHLEDYGEAPMETDGEHV

Parental  KRNCASVPEPLNLNPSLKHTLAQFHLSSQSSLGGPAAFSARYSQESMSPTVFLPLP-SPQVLPGPLLIPS
          KRNCASVPEPLNLNPSLKHTLAQFHLSSQSSLGGPAAFSARYSQESMSPTVFLPLP.SPQVLPGPLLIPS
Retrocopy KRNCASVPEPLNLNPSLKHTLAQFHLSSQSSLGGPAAFSARYSQESMSPTVFLPLP>SPQVLPGPLLIPS

Parental  DSSTELTQTVLEGESISCFQVGGEKRLCLPQVLNSVLREFSLQQINTVCDELYIYCSRCTSDQLHILKVL
          DSSTELTQTVLEGESISCFQVGGEKRLCLPQVLNSVLREFSLQQINTVCDELYIYCSRCTSDQ.HILKVL
Retrocopy DSSTELTQTVLEGESISCFQVGGEKRLCLPQVLNSVLREFSLQQINTVCDELYIYCSRCTSDQFHILKVL

Parental  GILPFNAPSCGLITLTDAQRLCNALLRPRTFPQNGSMLPAKNSLAQLKETGSAFEVEHECLGKCQGLFAP
          GILPFNAPSCGLITLTDAQRLCNALLRPRTFPQNGSML.AKNSLAQLKETGSAFEVEHECLGKCQGLFA.
Retrocopy GILPFNAPSCGLITLTDAQRLCNALLRPRTFPQNGSMLSAKNSLAQLKETGSAFEVEHECLGKCQGLFAL

Parental  QFYVQPDAPCIQCLECCGMFAPQTFVMHSHRSPDKRTCHWGFESAKWHCYLHVNQKYLGILEEKKLKIVL
          QFYVQPDAPCIQCLE.CGMFAPQTFVMHSHRSPDKRTCHWGFESAKWHCYLHVNQKYLGILEEKKLKIVL
Retrocopy QFYVQPDAPCIQCLESCGMFAPQTFVMHSHRSPDKRTCHWGFESAKWHCYLHVNQKYLGILEEKKLKIVL

Parental  EEMKEKFSMRNGKRTQXXTDTPSGMELQSWYPVIKQEADHVSQAHSFLHPSYYLYMCDKVVAPNVSLTSA
          EEMKEKFSMRNGKRTQ..TDTPSGMELQSWYPVIKQE.DHVSQAHSFLHPSY.LYMCDKVVAPNVSLTSA
Retrocopy EEMKEKFSMRNGKRTQSKTDTPSGMELQSWYPVIKQEGDHVSQAHSFLHPSYCLYMCDKVVAPNVSLTSA

Parental  VSQGKEVTKTEASRSILRQSEKPHSSGKHQKMVSYPDVSLEEQEKMDLKTSRELCSRSDSSISNNSASKK
          VS.GKEVTKTEASRSILR.SEKPHSSGKHQKMVSYPDVSLEEQEKMDLKTSRELCSRSDSSISNNSASKK
Retrocopy VS*GKEVTKTEASRSILRLSEKPHSSGKHQKMVSYPDVSLEEQEKMDLKTSRELCSRSDSSISNNSASKK

Parental  KSESTTCNFKIRDTTKM-GIGHVAAASSALLVKDVTCED
          KSESTTCNFK.RDTT.M...GHVAAA.S.LLVKDVTC.D
Retrocopy KSESTTCNFKTRDTTEM>KLGHVAAALSPLLVKDVTCVD

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	2.14 RPM	7.00 RPM
SRP012922_cerebellum	0.14 RPM	0.69 RPM
SRP012922_heart	0.23 RPM	1.16 RPM
SRP012922_kidney	0.55 RPM	2.19 RPM
SRP012922_liver	0.46 RPM	2.17 RPM
SRP012922_lung	1.83 RPM	9.16 RPM
SRP012922_quadricep_muscle	0.52 RPM	1.73 RPM
SRP012922_spleen	2.29 RPM	6.98 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_1589 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008923	1 retrocopy	retro_dnov_1589 ,
Ochotona princeps	ENSOPRG00000015606	1 retrocopy	retro_opri_960,