RetrogeneDB ID: retro_ogar_3269

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873760.1:435962..436792(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000015920
• Aliases: None
• Description: None

Sequence

>retro_ogar_3269
CAGCCTTTTGACAAGTGGTCATGTTTCTGTGTGAGACAAACAGAGAGTGCTGACAGATACAGAAATATTGTCATCAGGAA
GCAGAATGGCTTCACCCACATCTTGTTATCCACAAAATTATCAGAGAATAATTCTCTATATCCAGAGGTAATGAAAGAAG
TCCAGAGTGCTCTGATCATAGCAGCTGCTGACAACAGCAAGCTGGTTCTGCTCAGTGCAGTTGGCAGTGTTTTTTGTTGG
GTCTTGACTTTATTTATTTTATATGGCATTTAACAAATGACAGAAAAAGAGAAGCACTAAAATGGAAGAAGCTATAAGAA
ACTTCATGAATACTTTCATTCAGTTTAAGAAGTCCATTATTATAGTGGTAAATGGGCCCAGCCATTAGACTAGGAGCATC
CATATTGCCTCTTTGTGATGTGGTTTGGGCTAAGAAAAAGGCTTGGTCTCAAACACCCTATATTACCTTTGGACAGAGTC
CAGATGGCTGTTCTACCATTATGTTTCCCAACATTATGGAAGGAGCATCTGCAAATGAAATATAGCTTAGCGGGTGGAAG
CTGACCGCACAGGAGGCATGTAGCAAGGGCCTCGTCTTGCAGGTGTTCTGGCCCAGGACCTTCACCCAGGAAGTCATGGT
TGGAATTAAGGAGCTTGCCTCGTTTAATCCAGTTATGCTCGAGGAATCCAAAGCTCTTGTGCACTGTAACATGAAGATGG
AGCTGGAAAAGGCCAACAAGAAGGAATATGAAGTACTAAAGAAAATCTGGGGCTCTGCCCAAGGGATGGACTCCGGGTTA
AAGTACTTGCAGAGGAAGATCAATGAGTTT

Alignment

ORF - retro_ogar_3269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.79 %
• Parental protein coverage: 51.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QPFDKRLRFSVRQTESAYRYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMKEIQSALTTAAADDSKLVL
          QPFDK...F.VRQTESA.RYR.IV.RKQ.GFTHILLSTK.SENNSL.PEVMKE.QSAL..AAAD.SKLVL
Retrocopy QPFDKWSCFCVRQTESADRYRNIVIRKQNGFTHILLSTKLSENNSLYPEVMKEVQSALIIAAADNSKLVL

Parental  LSAVGSVFC-CGLDFIYFIRRLTDDRKRE-STKMAEAIRNFVNTFIQFKKPIIVAVNGP-AIGLGASILP
          LSAVGSVFC..GLDFIYFI..LT.DRKRE.STKM.EAIRNF.NTFIQFKK.II..VNGP.AI.LGASILP
Retrocopy LSAVGSVFC<LGLDFIYFIWHLTNDRKRE<STKMEEAIRNFMNTFIQFKKSIIIVVNGP>AIRLGASILP

Parental  LCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGT
          LCDVVWA..KAW.QTPY.TFGQSPDGCST.MFP.IM.GASANE..LSG.KLTAQEAC.KGLV.QVFWP.T
Retrocopy LCDVVWAKKKAWSQTPYITFGQSPDGCSTIMFPNIMEGASANEI*LSGWKLTAQEACSKGLVLQVFWPRT

Parental  FTQEVMVRIKELASCNPIVLEESKALVRCNMKMELEQANERECEVLKKIWGSAQGMDSMLKYLQRKIDEF
          FTQEVMV.IKELAS.NP..LEESKALV.CNMKMELE.AN..E.EVLKKIWGSAQGMDS.LKYLQRKI.EF
Retrocopy FTQEVMVGIKELASFNPVMLEESKALVHCNMKMELEKANKKEYEVLKKIWGSAQGMDSGLKYLQRKINEF

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_3269 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011787	1 retrocopy	retro_chof_525,
Callithrix jacchus	ENSCJAG00000021374	5 retrocopies	retro_cjac_2675, retro_cjac_3927, retro_cjac_4003, retro_cjac_4228, retro_cjac_4229,
Homo sapiens	ENSG00000153046	1 retrocopy	retro_hsap_4651,
Otolemur garnettii	ENSOGAG00000015920	2 retrocopies	retro_ogar_2406, retro_ogar_3269 ,
Pan troglodytes	ENSPTRG00000017688	1 retrocopy	retro_ptro_3090,