RetrogeneDB ID: retro_ogar_3082

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873711.1:57571..58234(-)
• Located in intron of: ENSOGAG00000004848

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMOD2
• Ensembl ID: ENSOGAG00000013745
• Aliases: None
• Description: tropomodulin 2 (neuronal) [Source:HGNC Symbol;Acc:11872]

Sequence

>retro_ogar_3082
ATCTATAATCTTGCAGCTGTCCTTGGAGTACACAATTTACTCAACATTCCAAAGTTTGATGAAGAAACAGCCAATAGTAA
AGATGGCAAAGGGCCTATAAGAAACGTGGTCAAAGGTGAGAAGGTCAAGCCAGTATTTGAGGAACCACCCAATCCCACAA
ATGTGGAAACAAGTCTACAGCAGATGAAAGCCAACAATCCTGGCCTGCAAGAAGTCAACCTCAACAACATTAAGAACATT
CCAGTTCCAACTCTGAAGGAATTTGCAAAGGCTCTGGAGACCAATACTCATGTAGAAAAGTTCAACCTGGCTGCAACCCG
CACCAATGACCCTGTGGCCATTGCTTTTGCAGATACATTGAAAGTAAACAAGACCTGGAAAAGTCTAAACATAGAATCCA
ATTTTATCACTGAAACTGGGATCCTGGCCCTGGTAGTTGCACTGAAAGAAAATGACACCTTGACAGAGATCAAGATGGGC
AACGAGAGGCAGCAGTTGGGAACAGCCTTAGAGATGGAAATTACCTAGATGCTGGAGGAGAATTCATGAATCCTCAATTT
TGGATATCAGTTTACCAAGAAAGGACCCCAAACAAGGGTGGCAGCTGCCATCACAAAGAATAGCAACCTGGTTCATAAGA
AGCGAGTTGAAGGAGACCCAAGG

Alignment

ORF - retro_ogar_3082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.52 %
• Parental protein coverage: 62.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYDLAAVLGVHNLLNNPKFDEETSNNKGGKGPVRNVVKGEKVKPVFEEPPNPTNVEMSLQQMKANDPSLQ
          .Y.LAAVLGVHNLLN.PKFDEET.N.K.GKGP.RNVVKGEKVKPVFEEPPNPTNVE.SLQQMKAN.P.LQ
Retrocopy IYNLAAVLGVHNLLNIPKFDEETANSKDGKGPIRNVVKGEKVKPVFEEPPNPTNVETSLQQMKANNPGLQ

Parental  EVNLNNIKNIPIPTLKEFAKALETNTHVKKFSLAATRSNDPVAIAFADMLKVNKTLKSLNIESNFITGTG
          EVNLNNIKNIP.PTLKEFAKALETNTHV.KF.LAATR.NDPVAIAFAD.LKVNKT.KSLNIESNFIT.TG
Retrocopy EVNLNNIKNIPVPTLKEFAKALETNTHVEKFNLAATRTNDPVAIAFADTLKVNKTWKSLNIESNFITETG

Parental  ILALVDALKENDTLTEIKIDNQRQQLGTAVEMEIAQMLEENSRILKFGYQFTKQGPRTRVAAAITKNNDL
          ILALV.ALKENDTLTEIK..N.RQQLGTA.EMEI..MLEENS.IL.FGYQFTK.GP.TRVAAAITKN..L
Retrocopy ILALVVALKENDTLTEIKMGNERQQLGTALEMEIT*MLEENS*ILNFGYQFTKKGPQTRVAAAITKNSNL

Parental  VRKKRVEGDRR
          V.KKRVEGD.R
Retrocopy VHKKRVEGDPR

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_3082 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000013745	1 retrocopy	retro_ogar_3082 ,