RetrogeneDB ID: retro_ogar_1686

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873561.1:2043243..2043792(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF3
• Ensembl ID: ENSOGAG00000006524
• Aliases: None
• Description: Kruppel-like factor 3 (basic) [Source:HGNC Symbol;Acc:16516]

Sequence

>retro_ogar_1686
CTCATGGTCTCCTTGTCAGAGGAGATGGAAAATTCAAATAGCAGCGTGCAAGTACCTGTAATTGAATCATACGAGAAGCC
TATATTACAGAAAAAAATTAAAATAGAACCTGGGATCAAACCACAGAGGACAGATATTTTCCTGAAGAAATGTCACCCCT
TTAATGAACTCAGTATCCTCCCCACCACCAGCATTGTTGCAAGAGAATCATCCTTCAGGCATTGTGCAGCCTGGGAAGAG
ACTTTACCTGTGGAATCCCCGGATACCCAGAGGAAGGGGCGGATACACAGATGCCATTACAACGGATGCAACAAGGTGTA
CACTAAAAGCTCCCACTTGAAAGCACACAGAAGAACATTCACACAGGAGAAAAACCTGACAGACAAACGGACATGGGAAG
GCTGCACATGGAAGTCTATGCGGTCTGATGAACTCATAAGATATTTCCGAAAACACACGGGAATCAAGCCTTTCCAGGGT
CCAGACTGTCACCGCGGCTTCTCCGGTTCTGACCATCTTGCCCTGCATAGGAAACGCCACATGCTAGTC

Alignment

ORF - retro_ogar_1686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.03 %
• Parental protein coverage: 52.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LMVSLSDEMENSNSSMQVPVIESYEKPILQKKIKIEPGIEPQRTD-YFPEEMSP-PLMNSV-SPPQALLQ
          LMVSLS.EMENSNSS.QVPVIESYEKPILQKKIKIEPGI.PQRTD.YFPEEMSP.PLMNSV.SPP.ALLQ
Retrocopy LMVSLSEEMENSNSSVQVPVIESYEKPILQKKIKIEPGIKPQRTD<YFPEEMSP<PLMNSVSSPPPALLQ

Parental  ENHPSVIVQPGKR-PLPVESPDTQRKRRIHRCDYDGCNKVYTKSSHLKAHRRTHTGEKPY--KCTWEGCT
          ENHPS.IVQPGKR..LPVESPDTQRK.RIHRC.Y.GCNKVYTKSSHLKAHRRT.T.EK....K.TWEGCT
Retrocopy ENHPSGIVQPGKR<TLPVESPDTQRKGRIHRCHYNGCNKVYTKSSHLKAHRRTFTQEKNLTDKRTWEGCT

Parental  WKFARSDELTRHFRKHTGIKPFQCPDCDRSFSRSDHLALHRKRHMLV
          WK..RSDEL.R.FRKHTGIKPFQ.PDC.R.FS.SDHLALHRKRHMLV
Retrocopy WKSMRSDELIRYFRKHTGIKPFQGPDCHRGFSGSDHLALHRKRHMLV

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_1686 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017488	1 retrocopy	retro_btau_271,
Choloepus hoffmanni	ENSCHOG00000004256	1 retrocopy	retro_chof_181,
Macaca mulatta	ENSMMUG00000003363	1 retrocopy	retro_mmul_2118,
Nomascus leucogenys	ENSNLEG00000017046	1 retrocopy	retro_nleu_2431,
Otolemur garnettii	ENSOGAG00000006524	1 retrocopy	retro_ogar_1686 ,