RetrogeneDB ID: retro_ogar_3259

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873758.1:1429656..1430552(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028467
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDCBP
• Ensembl ID: ENSOGAG00000013462
• Aliases: None
• Description: syndecan binding protein (syntenin) [Source:HGNC Symbol;Acc:10662]

Sequence

>retro_ogar_3259
ATTTCTCTCTATCCATCTTTTGAAGACTTGAAGGTAGATAAAGTAATTCAGGTTCAGACTGCCTTTTCTGCAAATCCTGC
CAACCCAGCAATTTTCTCAGAAGCTTCTGCTCCTGTCTCTCAAGATGGAAATCTCTATCCTAAACTGTATCCAGAGCTCT
CTCAGAACATGGGTGTGAGTTTAAATGAAGAAGAAATACGTGAAAATATGGCCATGGTCCCTGGAGCATCAGTTCAGGGG
CAATTGTTAGCAAAGCCTTCCAGTATGAGTTATATGGTAGCTCCTATAACTGGTAATGATGTTGGAATTTGTAGAGCAGA
AATTAAGCAAAGGATTCATGAAGTCATTTTTGTGTAAGCATCAAGATGGAAAAATTAGACTCAGGCTTAAATTGATAGAT
AATGGTATATTTTGTTCAGCTGATCCAGGCTAATTCTCCATCCTCTTTGGTTGGTCTGAGAGTTGAGGACCAGGTACTCC
AGATCATTGGTGAAAACTGTGCTGGCTGGAGCTCTGATAAAGCACACTATGTGCTCAAACAGGCTTTTGGAGAGAAGATT
ATTATGACCATTTGTGACAGGCCCTTTGAACGGACAATCACCATGCACAAAGATAGCAGTGGACATGTTGGCTTTATCTT
TAAAAATGGAAAAATAACATCCATAGTCAAAGATAGTTCTGCAGCCAGAAATGGCCCTCTCACGGAACACAACATCTGTG
AAATAAATGGGCAGAATGTCATTGTTTTGAAGGACTCTCAAATTGCAGACATACTGTCAACAGCTGGAACTTTAGTTACC
ATTATAATCATGCCTGCTTTTATCTTTGAACATATCATTAAATGGATGGCGCCAAGCATTATGAAAAGCCTGATGGACCA
CACCATTCCTGAAGTT

Alignment

ORF - retro_ogar_3259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPVSQDGNLYPKLYPELSQYMGLSLNEEEIFANM
          .SLYPS.EDLKVDKVIQ.QTAFSANPANPAI.SEASAPVSQDGNLYPKLYPELSQ.MG.SLNEEEI..NM
Retrocopy ISLYPSFEDLKVDKVIQVQTAFSANPANPAIFSEASAPVSQDGNLYPKLYPELSQNMGVSLNEEEIRENM

Parental  VLVGGAPAQGQLVARPSSMSYMVAPVTGNDVGIRRAEIKQGIREVI-LCKDQDGKIGLRLKSIDNGIF-V
          ..V.GA..QGQL.A.PSSMSYMVAP.TGNDVGI.RAEIKQ.I.EVI.LCK.QDGKI.LRLK.IDNGIF.V
Retrocopy AMVPGASVQGQLLAKPSSMSYMVAPITGNDVGICRAEIKQRIHEVI>LCKHQDGKIRLRLKLIDNGIF>V

Parental  QLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSSGH
          QL.QANSP.SLVGLR..DQVLQI.GENCAGWSSDKAH.VLKQAFGEKI.MTI.DRPFERTITMHKDSSGH
Retrocopy QLIQANSPSSLVGLRVEDQVLQIIGENCAGWSSDKAHYVLKQAFGEKIIMTICDRPFERTITMHKDSSGH

Parental  VGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTARTVVTITVMPTFIFEHI
          VGFIFKNGKITSIVKDSSAARNG.LTEHNICEINGQNVI.LKDSQIADILSTA.T.VTI..MP.FIFEHI
Retrocopy VGFIFKNGKITSIVKDSSAARNGPLTEHNICEINGQNVIVLKDSQIADILSTAGTLVTIIIMPAFIFEHI

Parental  IKRMAPSIMKSLMDHTIPEV
          IK.MAPSIMKSLMDHTIPEV
Retrocopy IKWMAPSIMKSLMDHTIPEV

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_3259 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259 ,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,