RetrogeneDB ID: retro_ogar_3493

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873937.1:73257..74012(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP29
• Ensembl ID: ENSOGAG00000013003
• Aliases: None
• Description: synaptosomal-associated protein, 29kDa [Source:HGNC Symbol;Acc:11133]

Sequence

>retro_ogar_3493
ATGTCGGCCTACCCCAAAAGCTACAACCCGTTCGATGACGACATGGAAGACGAGGGCATCCAGCCGGCCCCCTGGAGGGA
CGCCCGTGACCCCTCCAACGGGCCGTGGACAGGCAGCAGTACCTGCGGCAGGAGGTGCTGCGCAGGGCCGAGGCTACTGT
TGCCAGCACCAGCAGGTCCCCGTCGTCATGTACGAGAAAGCCGGGGTCGCCACTTCCATGGAACTTGTCTGTCAGTGAGG
AGTCTTAGAACGCACAGAGAAGATAGTGGATAAGATGGACCAGGATTGAAGACCAGTCAGAAGTACATCAACAGCATTAA
GAGTGTGTTTGGGGGGCTCGTCAATTACTTCAAGTCCAAACCTGTAAGACCCCACCTGAACAGAATGGCACCCTCACCCT
CCAAGTCAGCAATAGATTAAAAGAAGCTATAAGTACAAGTAAAGAACAGGAGGCAAAGTACCAGGCCAGCCACCCAAACC
TCTTAAAGCTGGATGATGTAGACACTGTTGCTGGAGGGGCTAGTTCTACTGTGAGCACTGATGCTTACCCGAAGAACCCA
CACCTTCGAGCCTATCACCAGAAGATCCATAGCAACCTGGATGAGCTGTCCGTGTGACTGGGCCGTCTGAAAGGCATAGC
CCTGGGGATACAGATGGAAATTGAGGAACAAGACTACATTCTTGACCGACTGACAACCAAAGTGGACAAGTTAGACATTA
ATATAAAAAGCACAGAAAGAAAAGTTCAACAACTC

Alignment

ORF - retro_ogar_3493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSAYPKSYNPFDDDVEDEGTQPAPWRDARDSSDGPTEP-ADRQQYLRQEVLRRAEATVASTGRSLS-LVY
          MSAYPKSYNPFDDD.EDEG.QPAPW...RD..D....P..DRQQYLRQEVLRRAEATVAST.RS.S...Y
Retrocopy MSAYPKSYNPFDDDMEDEGIQPAPW---RDARDPSNGP<VDRQQYLRQEVLRRAEATVASTSRSPS<VMY

Parental  ESEKAGVATSEELVRQRGVLERTEKIVDKMDQD-LKTSQKHINSIKSVFGGLVNYFKSKP-AETPPEQNG
          E..KAGVATS.ELV.Q.GVLERTEKIVDKMDQD.LKTSQK.INSIKSVFGGLVNYFKSKP...TPPEQNG
Retrocopy E--KAGVATSMELVCQ*GVLERTEKIVDKMDQD<LKTSQKYINSIKSVFGGLVNYFKSKP<CKTPPEQNG

Parental  TLTPQASNRLKEAISTSKEQEAKYQASHSNLRKLDDVDSDTVAGGASSTASTDAYPKNPHLRAYHQKIDS
          TLT.Q.SNRLKEAISTSKEQEAKYQASH.NL.KLDDV..DTVAGGASST.STDAYPKNPHLRAYHQKI.S
Retrocopy TLTLQVSNRLKEAISTSKEQEAKYQASHPNLLKLDDV--DTVAGGASSTVSTDAYPKNPHLRAYHQKIHS

Parental  NLDELSLGLGRLKGIALGMQTEIEEQDDILDRLTTKVDKLDINIKSTERKVRQL
          NLDELS..LGRLKGIALG.Q.EIEEQD.ILDRLTTKVDKLDINIKSTERKV.QL
Retrocopy NLDELSV*LGRLKGIALGIQMEIEEQDYILDRLTTKVDKLDINIKSTERKVQQL

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_3493 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015201	1 retrocopy	retro_cfam_1542,
Cavia porcellus	ENSCPOG00000003137	1 retrocopy	retro_cpor_1442,
Dasypus novemcinctus	ENSDNOG00000005913	4 retrocopies	retro_dnov_1401, retro_dnov_1855, retro_dnov_2001, retro_dnov_2364,
Nomascus leucogenys	ENSNLEG00000000108	1 retrocopy	retro_nleu_2645,
Otolemur garnettii	ENSOGAG00000013003	1 retrocopy	retro_ogar_3493 ,