RetrogeneDB ID: retro_ogar_2306

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873610.1:4382870..4383873(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNIP1
• Ensembl ID: ENSOGAG00000008634
• Aliases: None
• Description: Smad nuclear interacting protein 1 [Source:HGNC Symbol;Acc:30587]

Sequence

>retro_ogar_2306
GCCGGCGAACCGGGCCGCCCCAGCTACCGTGGGAGCCGAGCCCGAGGAGTTAGCCAGTCCCCAGCGGAAAAGAAAAACAG
GTCCTCAGGGAGAAGAAGCAAGTCTCCTCGGAGTAAGAGAAGCCGAAGTCCTCATCACTCGACTGTCAAAGTGAAGCAGG
AACGTGATGATCATCCCCGGATAGGACAGGAGGATGGGCAGCACCGGGAACCTTCAGAGCAGGAACACAGATCTAGGAAC
AGTGACCAAGACAGACACCGGAGCTATTCCCACCAAAGCAGAACCCCTGGGAGTGGGCAGGCTCAAGGATGGGATCGGGA
CATTCAGAAGCTTCAGATTCAAGAAGAGCCGGAGTTTTATAATGCCAGACGCCGGGAGCATCGCCAGAAGAATGAAGTTA
GTGGCAGTGGTAATGAGTCTCAGGAGGTGGTTCCTCGGCCTGGTGGCAACAACAAAGAAAAAGAGGTTCCTGTTAAAGAA
AAGCCAAGTTTTGAACTCTTTGGGGCCCTTCCTGAGGATACCAACACCTTCCGAGGTGTAGTCATTAAGTATAGTGAGCC
CCCAGAAGCACGTATCCTCAAAAAAAAGGTGGCGTCTCTACTCATTTAAAAATGATGAGGTCCTTCCAGTCATGTACATA
CATCGACAAAGTGCGTACCTCCTGGGTGGACACTGACGCATTGCGGATATTCCAATTGATTATCCGTCTTGTTCAAAGCA
GCATTTGGTCTTTCAGTATCGGCTTGTGGAATATACTGGTGTTGATGGCACAGTTGGTCGAAGAGTGAAGCCCTACGTCA
TTGACCTTGGCTCAGGCAATGGCACTTTCCTAAACAACAAACGTATTGAGCCACAGAGATAATATGAACTTAAAGAAAAG
GATGTACTCAAGTTTGGGTTCAGTAGCAGAGAATATGTCTTGCTGCATTAGTCATCAGATACTTCTGAAATAGACAGGAA
AGAAGATGAGGATGATGAAGAGGAGGAGGAAGTGTCTGACAGC

Alignment

ORF - retro_ogar_2306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 86.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGEPGRPSHRGSRARGVSRSPAKKKNKSSGRRSKSPRSKRSRSPHHSTVKVKQERDDHPRRGREDRQHRE
          AGEPGRPS.RGSRARGVS.SPA.KKN.SSGRRSKSPRSKRSRSPHHSTVKVKQERDDHPR.G.ED.QHRE
Retrocopy AGEPGRPSYRGSRARGVSQSPAEKKNRSSGRRSKSPRSKRSRSPHHSTVKVKQERDDHPRIGQEDGQHRE

Parental  PSQQEHKRSRNSDRDRHRSYSRQRRTPGSGQAQGRDRDIQELQIQEEEREFYNARRREHRQKNEVSGSGT
          PS.QEH.RSRNSD.DRHRSYS.Q.RTPGSGQAQG.DRDIQ.LQIQEE..EFYNARRREHRQKNEVSGSG.
Retrocopy PSEQEH-RSRNSDQDRHRSYSHQSRTPGSGQAQGWDRDIQKLQIQEEP-EFYNARRREHRQKNEVSGSGN

Parental  ESQEVVPRPGGNNKEKEVPVKEKPSFELSGALLEDTNTFRGVVIKYSEPPEARI-PKKRWRLYPFKNDEV
          ESQEVVPRPGGNNKEKEVPVKEKPSFEL.GAL.EDTNTFRGVVIKYSEPPEARI.....WRLY.FKNDEV
Retrocopy ESQEVVPRPGGNNKEKEVPVKEKPSFELFGALPEDTNTFRGVVIKYSEPPEARI>XXXXWRLYSFKNDEV

Parental  LPVMYIHRQSAYLLGRHRRIADIPIDHPSCSKQHAVFQYRLVEYTRADGTVGRRVKPYIIDLGSGNGTFL
          LPVMYIHRQSAYLLG.H.RIADIPID.PSCSKQH.VFQYRLVEYT..DGTVGRRVKPY.IDLGSGNGTFL
Retrocopy LPVMYIHRQSAYLLGGH*RIADIPIDYPSCSKQHLVFQYRLVEYTGVDGTVGRRVKPYVIDLGSGNGTFL

Parental  NNKRIEPQRYYELKEKDVLKFGFSSREYVLLHESSDTSEIDRKEDEDDEEEEEVSDS
          NNKRIEPQR.YELKEKDVLKFGFSSREYVLLH.SSDTSEIDRKEDEDDEEEEEVSDS
Retrocopy NNKRIEPQR*YELKEKDVLKFGFSSREYVLLH*SSDTSEIDRKEDEDDEEEEEVSDS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2306 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001963	1 retrocopy	retro_cjac_1094,
Myotis lucifugus	ENSMLUG00000017132	2 retrocopies	retro_mluc_1400, retro_mluc_159,
Mus musculus	ENSMUSG00000050213	2 retrocopies	retro_mmus_3038, retro_mmus_941,
Otolemur garnettii	ENSOGAG00000008634	2 retrocopies	retro_ogar_2306 , retro_ogar_893,