RetrogeneDB ID: retro_dnov_1045

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_14047:9770..10580(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGOL1
• Ensembl ID: ENSDNOG00000008694
• Aliases: None
• Description: shugoshin-like 1 (S. pombe) [Source:HGNC Symbol;Acc:25088]

Sequence

>retro_dnov_1045
AGACATAAAGAAACGAAAGAAAGAGAAAAGGAATAAAAACTTGGAAGAAATTGGCAAGCGCAAGTCTTTGATAGCTGCCC
CGTGCCAAACAGCACTTCTACACTCCTGAAAAATTACCAGGACAACAATAGAATGTTAGTTTTAGCTTTGGAAAATGAAA
AATCCAAAGTGAGAGAAGCCCAAGATATCATCCTAGAGCTCAGAAAAGAATGTTATTACCTCACATGCCAGTTCTATGCA
TTGAAAGAAAAACTTACTTGACAAGAAACTGAAGAACCTGCTCAGAGTCTGGACGTATGTCCCTCTGGAATGGACTCCAT
TAGTAATGACAACTCCAGGGAATTATTTGTGAAGAATTTACGGCAAAGTCCTCTTCAGGAAGCTGGCCCTCCAGGGCAGG
AAGAGTCATTCCAAAGAGAAGAGCAAACTCCTACTGTTTCAGACAAATTGGGACTTGATTTTGAGTCAAGTGAAGATAAG
CCTACTGATCAGGTCTTACCTAGAACTGTATCTGTTCGTCACAATTTAAAAAAGCGTTTTAACAGTCTATGCCAATTTGA
TGCTGTGGATAACTTTGAAACCAGTCATTTGACCATAGAATCTTTTAAATTAGAAAGAATTCGCTTTGCTGACCCATTTA
TAAATCTACACATATCTGAAAATGTAGACCAAAACATTTCTCAGGGGAACAAGGACCAAATTAACTTACCACCAAAACCG
ATTTACCCAGCAAGTCTTAATAAAACAAAAGAAGTCATTTTAGAGTCTAAATCTGAGCAAACTAAAACTAAGCGTATAGA
TGCACAAAGA

Alignment

ORF - retro_dnov_1045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.78 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RMKEKRNKNLE-EIGKR-KSLIAAPCQVINSTSTLLKNYQDNNRMLVLALENEKSKVREAQDIILELRKE
          R.KE......E...G..........C.V.NSTSTLLKNYQDNNRMLVLALENEKSKVREAQDIILELRKE
Retrocopy RHKETKEREKE*KLGRNWQAQVFDSCPVPNSTSTLLKNYQDNNRMLVLALENEKSKVREAQDIILELRKE

Parental  CYYLTCQLYALKEKLTSQETEEPAQSLEVCPSGMDSISNDNSRELFVKDLRQSPLQEAGPRGQEESFQRE
          CYYLTCQ.YALKEKLT.QETEEPAQSL.VCPSGMDSISNDNSRELFVK.LRQSPLQEAGP.GQEESFQRE
Retrocopy CYYLTCQFYALKEKLT*QETEEPAQSLDVCPSGMDSISNDNSRELFVKNLRQSPLQEAGPPGQEESFQRE

Parental  EQTPTVSDRLGFDFESSEDKPTDHVLPRTVSVRHNLKKRFNSLCQFDAVDNFETSHLTVESFKLERIRFA
          EQTPTVSD.LG.DFESSEDKPTD.VLPRTVSVRHNLKKRFNSLCQFDAVDNFETSHLT.ESFKLERIRFA
Retrocopy EQTPTVSDKLGLDFESSEDKPTDQVLPRTVSVRHNLKKRFNSLCQFDAVDNFETSHLTIESFKLERIRFA

Parental  DPFINLHISENVDQNISQGNKDQINLPPKPIYPASLSKAKEVILESKSEQTKTKRIDAQR
          DPFINLHISENVDQNISQGNKDQINLPPKPIYPASL.K.KEVILESKSEQTKTKRIDAQR
Retrocopy DPFINLHISENVDQNISQGNKDQINLPPKPIYPASLNKTKEVILESKSEQTKTKRIDAQR

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	2.72 RPM	10.11 RPM
SRP012922_cerebellum	0.41 RPM	2.75 RPM
SRP012922_heart	0.00 RPM	1.39 RPM
SRP012922_kidney	0.00 RPM	3.01 RPM
SRP012922_liver	0.15 RPM	0.93 RPM
SRP012922_lung	1.68 RPM	7.79 RPM
SRP012922_quadricep_muscle	0.17 RPM	0.52 RPM
SRP012922_spleen	7.78 RPM	27.93 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_1045 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013948	1 retrocopy	retro_chof_2699,
Dasypus novemcinctus	ENSDNOG00000008694	1 retrocopy	retro_dnov_1045 ,
Equus caballus	ENSECAG00000012475	1 retrocopy	retro_ecab_846,
Mus musculus	ENSMUSG00000023940	2 retrocopies	retro_mmus_3486, retro_mmus_867,
Rattus norvegicus	ENSRNOG00000022499	1 retrocopy	retro_rnor_2440,