RetrogeneDB ID: retro_dnov_2365

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_67543:12620..13612(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC6
• Ensembl ID: ENSDNOG00000011590
• Aliases: None
• Description: cell division cycle 6 [Source:HGNC Symbol;Acc:1744]

Sequence

>retro_dnov_2365
ATGCCTCGAACCCGATCCCAGTCACAGGTCACAATTAATTTTCCAAAAAAGAAGCCATCTTGGACAGTGGACAAAGCTAA
AAATTGTGGTGACACCAAACTAGAACTGACAAATGTGCAGGCTATCCCTTGTTCTCCTTGTGTAAAAATTCAGCCTCTTA
GCCCCAGAAAACGTCTAGGTGATGACAACTTGTGTAACACTCCCCATTTGACTCCCTGTTCTCCACCAAAGCAAGGCAAG
AAAGAGAATGGTCACCCTCGCTCACATACACCTAAGGGCGCAGATTGCTATTTGACAATCAGCTAAAAGTTAAGTCTCCT
AGCGAAAGAGAACAGGCCAGAGTTCACCAAAGTAAAACGCTTTCCTCAGTTCAAAAACGTCAAGAGATCACAACAAATTC
TGAGCAGAAATGTCTACTGGAGAAACAATCTGCATGTGTGAGACTGTTCAAGCAAGAAGGCACTTGCTACCAACAAGCAA
AGCTAGTCCTGAATACAGCTGTCCCAGATCGGCTCCTTGCCAGGGAAAAGGAGATGGATGTCATCAGGAATTTCCCGAGG
GAGCACATCTGTGGGAAAAAAGCTGGAAGTCTTTATCTTTCTGGTGCTCCTGGAACTGGAAAAACTGCCTGCTTAAGCCG
AATTCTGCAAGACCTCAAGAAGGAACTGAAAGGCTTTGAAACTATCAGGCTGAATTGCATGTCCTTGAGGAGTGCCCAGG
CTGTATTCCCAGCTATTGCTCAGGAGATTTGTCAGGAAGAAGTATCCAGGACAGCTGGGAAGGACATGATGAAGAAGTTG
GAAAAACATATGAGTGCAGAGAGGGGCCCCATGATCTTGTTGGTGTTGGACGAGATGGATCAGCTGGACAGCAAAGGGCA
GGATGTATTATACACACTGTTTGAATGGCCATGGCTAAGCAACTCTCGACTGGTGTTAATTGGTATAGCTAATACTCTGG
ATCTCACAATCAGAATTCTGCCTAGGCTTCAA

Alignment

ORF - retro_dnov_2365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.99 %
• Parental protein coverage: 62.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPRTRSQSQVTINFPKKKPSWTLDKAKNCGDTKLELTNVQAIPCSPCVKILPLSPRKRLGDDNLCNTPHL
          MPRTRSQSQVTINFPKKKPSWT.DKAKNCGDTKLELTNVQAIPCSPCVKI.PLSPRKRLGDDNLCNTPHL
Retrocopy MPRTRSQSQVTINFPKKKPSWTVDKAKNCGDTKLELTNVQAIPCSPCVKIQPLSPRKRLGDDNLCNTPHL

Parental  PPCSPPKQGKKENGHPRSHTPKG-RRLLFDNQLKVKSPSEREQARVHQSKTLSSVQKGQEITTNSEQKCL
          .PCSPPKQGKKENGHPRSHTPKG.RRLLFDNQLKVKSPSEREQARVHQSKTLSSVQK.QEITTNSEQKCL
Retrocopy TPCSPPKQGKKENGHPRSHTPKG<RRLLFDNQLKVKSPSEREQARVHQSKTLSSVQKRQEITTNSEQKCL

Parental  LEKQSACVRLFKQEGTCYQQAKLVLNTAVPDRLPAREKEMDVIRNFLREHICGKKAGSLYLSGAPGTGKT
          LEKQSACVRLFKQEGTCYQQAKLVLNTAVPDRL.AREKEMDVIRNF.REHICGKKAGSLYLSGAPGTGKT
Retrocopy LEKQSACVRLFKQEGTCYQQAKLVLNTAVPDRLLAREKEMDVIRNFPREHICGKKAGSLYLSGAPGTGKT

Parental  ACLSRILQDLKKELKGFKTIMLNCMSLRSAQAVFPAIAQEICQEEVSRTAGKDMMKKLEKHMSAERGPMI
          ACLSRILQDLKKELKGF.TI.LNCMSLRSAQAVFPAIAQEICQEEVSRTAGKDMMKKLEKHMSAERGPMI
Retrocopy ACLSRILQDLKKELKGFETIRLNCMSLRSAQAVFPAIAQEICQEEVSRTAGKDMMKKLEKHMSAERGPMI

Parental  LLVLDEMDQLDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLQ
          LLVLDEMDQLDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLT.RILPRLQ
Retrocopy LLVLDEMDQLDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTIRILPRLQ

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	18.28 RPM
SRP012922_cerebellum	0.00 RPM	2.61 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	4.65 RPM
SRP012922_liver	0.00 RPM	0.46 RPM
SRP012922_lung	0.00 RPM	1.99 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.00 RPM	18.89 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_2365 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	ENSDNOG00000011590	1 retrocopy	retro_dnov_2365 ,
Mus musculus	ENSMUSG00000017499	1 retrocopy	retro_mmus_3570,