RetrogeneDB ID: retro_ogar_893

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:12074561..12075639(+)
• 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_893
GTGAAGCAGGAGCGTCTCAGCTTGGAAGCTGCACCTCCGGCCCACCGCGGCCCAGACTTCTCTGGTTGCCGCTCGTCCCC
ACCGGCCGGCCAGCTGGGCCGCCCCACCACCATGGAAGCCGAGCTCGAGGAGTTAGCTAATCCCCAGTCAAAAAGAAAAA
TGAGTCCTCAGGGAGAAGAAGCAAGACTCCTCTCAATAAGAGAAGCCAAAGTCCTCACTACTCAACAGTCAAAGTGAAGC
AGGAACGTGAGGGTCATCCCCAGAGAGGACGGAAGGATCAGCAGCACTTGGAACCTTCAGGGCAGGAACCCAAGTGATCT
AGGAACAGTGACCAAGACAAGACACCAGAGCTATTCCCATCAAAGGAGAACCTCTAACGAGAGGCCTGGGAGTGGGCAGG
CTCAGGGATGACAGGATCCGGACATTCAGAAGCTTCAGGCTCAAGAAGAAGAGCGGGAGTTTTATAATGCCAGACACCGG
GAGCATCACCAAAAGAATGACGGTGGTGGCTGTGGTAATGAGTCTCAGGAGGTGGTTCCTCGGCCTGGTGGCAACAACAA
AGAAAAAAAGGTTCCTGTTAAAGAAAAACCAAGTTTTGAACTTTCTGGGACCTTCTTGAAGACACTAACACTTTCCAAGG
TGTAGTCATTAAATATAGTGAGCCCCCAGAAGCATGTATCCCCCCCAAACAGTGGCGTCTCTACCCATTTAAAATGATGA
GGTATTTCCGGTCATGTACATTCATCGACAAAGTGCGTACCTCCTAGGTCGACCCTAACGTATCTCGGACATTCCAACTG
ATCATCCTTCTTGTTCAAAGTAGCATGCGGTCTTTCAGTATCAGCTTGTGGAATAGACTTGTGCTGATGGCACAGTTGGT
GGAAGAGTGTAGCCCTACGTTTACCTTGGCTCAGGCAATGGCAACTTCTTAAACATCAAATATATTGAGCTACAGAGATA
CTATGAACTTAAAGAAAAGGATGTACTCAAGTTTGGGTTCAGTAACAGAGAATATGTCTTGCTCCATGAGTCGTCAGACC
CTTCTGAAATAGACAGGAAAGAAGATGGGGATGAGGAA

Alignment

ORF - retro_ogar_893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.18 %
• Parental protein coverage: 91.28 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VKQERLSPEAAPPAHRRPDFSGSGSSPPAGEPGRPS-HRGSRARGVSRSPAKKKNKSSGRRSKSPRSKRS
          VKQERLS.EAAPPAHR.PDFSG..SSPPAG..GRP..H.GSRARGVS.SP.KKKN.SSGRRSK.P..KRS
Retrocopy VKQERLSLEAAPPAHRGPDFSGCRSSPPAGQLGRPT<HHGSRARGVS*SPVKKKNESSGRRSKTPLNKRS

Parental  RSPHHSTVKVKQERDDHPRRGREDRQHREPSQQEHKRSRNSDRD-RHRSYSRQRRT----PGSGQAQG-R
          .SPH.STVKVKQER..HP.RGR.D.QH.EPS.QE.K.SRNSD.D.RH.SYS.QRRT....PGSGQAQG..
Retrocopy QSPHYSTVKVKQEREGHPQRGRKDQQHLEPSGQEPK*SRNSDQD>RHQSYSHQRRTSNERPGSGQAQG*Q

Parental  DRDIQELQIQEEEREFYNARRREHRQKNEVSGSGTESQEVVPRPGGNNKEKEVPVKEKPSFELSGA-LLE
          D.DIQ.LQ.QEEEREFYNAR.REH.QKN...G.G.ESQEVVPRPGGNNKEK.VPVKEKPSFELSG..LLE
Retrocopy DPDIQKLQAQEEEREFYNARHREHHQKNDGGGCGNESQEVVPRPGGNNKEKKVPVKEKPSFELSGT<LLE

Parental  DTNTFRGVVIKYSEPPEARIPKKRWRLYPFK-NDEVLPVMYIHRQSAYLLGRHRRIADIPIDHPSCSKQH
          DTNTF.GVVIKYSEPPEA.IP.K.WRLYPFK.NDEV.PVMYIHRQSAYLLGR..RI.DIP.DHPSCSK.H
Retrocopy DTNTFQGVVIKYSEPPEACIPPKQWRLYPFK<NDEVFPVMYIHRQSAYLLGRP*RISDIPTDHPSCSK*H

Parental  AVFQYRLVEYTRADGTVGRRVKPYIIDLGSGNGTFLNNKRIEPQRYYELKEKDVLKFGFSSREYVLLHES
          AVFQY.LVE.T.ADGTVG.RV.PY...LGSGNG.FLN.K.IE.QRYYELKEKDVLKFGFS.REYVLLHES
Retrocopy AVFQYQLVE*TCADGTVGGRV*PYVY-LGSGNGNFLNIKYIELQRYYELKEKDVLKFGFSNREYVLLHES

Parental  SDTSEIDRKEDEDDE
          SD.SEIDRKED.D.E
Retrocopy SDPSEIDRKEDGDEE

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_893 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 ,