RetrogeneDB ID: retro_ogar_3312

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873775.1:66404..67253(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYAP1
• Ensembl ID: ENSOGAG00000028403
• Aliases: None
• Description: synapse associated protein 1 [Source:HGNC Symbol;Acc:16273]

Sequence

>retro_ogar_3312
CAAAAATTAACTGAATCAGTTGCTGAGACTACTCAAACAATAAAGAAGTCAGTAGAAGAAGGAAAAATAGATGACATCTT
TGATAAGACAATTATAGGAGATTTTCATACGGAACAGAAGAAATTTGTTGAAGAGCAGCATACAAAGAAGTCAGAAGCAG
CCGTGCTCCCATGGGTTGATAGTAACGATGAAGAAACAATTCAACAACAAATCCTGGCCTTATCTTCTGGCAAGAGGAAT
TTCCTTCGTGACCCTCCAGCTGGAGTGCAGTTTAATTTTGACTTTGATCAGATGTACCCTGTTGCCCTGGTCATGCTCCA
AGAGAATGAACTACTGAGCAAGATGAGATTCGCCCTAGTTCCTAAACTGGTGAAGGAGTAAGTGTTTTGGAGGAACTACT
TTTACTGTGTATCCCTGATTAAGCAGCCGGCCCAGTTCACTGCCCTGGCCGCCCAGCAGCAGGCAGCGGAGAAGGAGGAG
AAGAACAGCTGCAGGCAGGAGCATTAGCAGCGGGCAGAGGCAGTATGGCCCAAAACACCACCTGTTGTAATCAAATCTCA
GCTTAAAACTCAAGAGGATGAGGAAGAAATTTCTACTAGTCCAGGTGTTTCTGAGTTTGTCAGTGATGCCTTTGATGCCT
GTAACCTTAATCAAGAAGATCTAAGAAAAGAAATGGAACAACTAGTGCTTGACAAAAAGCAAGAGAAGACCACTGCTCCG
GAAGAGGATTCTGCAGACTGGGAAAAAGAACTACAACAGGAACTTCAAGAATATGAAGTGGTGGCAGAATCAGAAAAACG
CGATGAAAACTGGGATAAGGAAATAGAGAAAATGCTGCAAGAGGAAAAT

Alignment

ORF - retro_ogar_3312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 79.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKLTESVAETAQTIKKSVEEGKIDDIFDKTIIGDFHKEQKKFVEEQHTKKSEAAVPPWVDSNDEETIQQQ
          .KLTESVAET.QTIKKSVEEGKIDDIFDKTIIGDFH.EQKKFVEEQHTKKSEAAV.PWVDSNDEETIQQQ
Retrocopy QKLTESVAETTQTIKKSVEEGKIDDIFDKTIIGDFHTEQKKFVEEQHTKKSEAAVLPWVDSNDEETIQQQ

Parental  ILALSADKRNFLRDPPAGVQFNFDFDQMYPVALVMLQEDELLSKMRFSLVPKLVKEEVFWRNYFYRVSLI
          ILALS..KRNFLRDPPAGVQFNFDFDQMYPVALVMLQE.ELLSKMRF.LVPKLVKE.VFWRNYFY.VSLI
Retrocopy ILALSSGKRNFLRDPPAGVQFNFDFDQMYPVALVMLQENELLSKMRFALVPKLVKE*VFWRNYFYCVSLI

Parental  KQSAQLTALAAQQQAAEKEEKNSSRQEDSQLAEAVRPKTPPVVIKSQLKTQEDEEEISTSPGVSEFVSDA
          KQ.AQ.TALAAQQQAAEKEEKNS.RQE..Q.AEAV.PKTPPVVIKSQLKTQEDEEEISTSPGVSEFVSDA
Retrocopy KQPAQFTALAAQQQAAEKEEKNSCRQEH*QRAEAVWPKTPPVVIKSQLKTQEDEEEISTSPGVSEFVSDA

Parental  FDACNLNQEDLRKEMEQLVLDKKQEKTTVLEEDSADWEKELQQELQEYEVVAESEKRDENWDKEIEKMLQ
          FDACNLNQEDLRKEMEQLVLDKKQEKTT..EEDSADWEKELQQELQEYEVVAESEKRDENWDKEIEKMLQ
Retrocopy FDACNLNQEDLRKEMEQLVLDKKQEKTTAPEEDSADWEKELQQELQEYEVVAESEKRDENWDKEIEKMLQ

Parental  EEN
          EEN
Retrocopy EEN

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_3312 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	ENSOGAG00000028403	1 retrocopy	retro_ogar_3312 ,