RetrogeneDB ID: retro_ogar_1858

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873570.1:8960603..8961355(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPDC1
• Ensembl ID: ENSOGAG00000002689
• Aliases: None
• Description: neural proliferation, differentiation and control, 1 [Source:HGNC Symbol;Acc:7899]

Sequence

>retro_ogar_1858
CCAGGAGCCCATGCCTGTGAGCCTTGTCTGTAGCCCTTCCAGGAGGACCATCAAGGGTTATGTGTGTTCAGAATTCCACA
GCCTCCAGGAAAGGACCAGCCCCAACCCAGAGTGAAAAATAAAATTAACTTCCTGGCCCAGGACTTATCCCGGAAGGGGG
CAGGGCATTGAAGTCTCACAGCTCCACACCTGGCCACAGCCAGACAGCAGCTAGCTCCCAGAGGCTGCAGCCACTCTGGG
GTTCTGAGAGCTGGGTCAAGGACTCGAACCTGGTCTCCTGTCAACACAGGGAGCCCCTGTGCCCATATCCCATACTTCCT
GGGTCTCCCATATGTCCTCTAGGCCAGTGCACATTGTCCCCCCGGAACCCTGAGGTGAGCACAGGACAGCCTCACCTTTG
TACTAATTGTAGCCTTCTGCATGGCTTGTAGCGCTTCCCTTGCTGTGGCAACTATATACTGGTACAGGCTGCAGTGAGCC
ATCTGCCTGACCCAGAAGGCAGGCTATGCAGCCCCAAAGGCTCCCAACTCGCCTGTGGCACCTCGGATGTCACCTAGTGA
CCAGTAGCTGATACAGAGCATGAAGATGTACACTATCAGCACCAGAGACAGCAGATACTGAGCCTAAAGCGGGATAAAGA
GTTCAAGAAATTGGATTCAGCATCCTCTGACGAGAACGAAGATGGCAACTTCACAGTGTATGAGGGCCCTGACCTAGCCC
TGACTGGAGAGATGGAAGTGCACACCCCCCTG

Alignment

ORF - retro_ogar_1858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.94 %
• Parental protein coverage: 65.03 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGAHACGPCLRPFQEDQQGLCVLRVRQPPGKDRSQPRLEDEIDFLAQKLARKGAGHWSLTAPPLPKARQR
          PGAHAC.PCL.PFQED.QGLCV.R..QPPGKD..QPR....I.FLAQ.L.RKGAGH.SLTAP.L..ARQ.
Retrocopy PGAHACEPCL*PFQEDHQGLCVFRIPQPPGKDQPQPRVKNKINFLAQDLSRKGAGH*SLTAPHLATARQQ

Parental  L-PEAAA-TLGFSELGQGLEPGLLSTQGAPVPTSHTSWGSPVSSGPVHMSPLEPRHEHR-DSLTFVLIVA
          L.P.....TLGF.ELGQGLEPGLLSTQGAPVP.SHTSW.S..SS.PVH..P.EP..EHR.DSLTFVLIVA
Retrocopy LAPRGCS>TLGF*ELGQGLEPGLLSTQGAPVPISHTSWVSHMSSRPVHIVPPEP*GEHR<DSLTFVLIVA

Parental  FCVAGGAALAMATVCWCRLQRAIHLTQKADYAAPKAPSSPVAPRMSPGDQRLAHSAEMY-HYQHQRQQML
          FC.A..A.LA.AT..W.RLQ.AI.LTQKA.YAAPKAP.SPVAPRMSP.DQ.L..S..MY.HYQHQRQQ.L
Retrocopy FCMACSASLAVATIYWYRLQ*AICLTQKAGYAAPKAPNSPVAPRMSPSDQ*LIQSMKMY<HYQHQRQQIL

Parental  SLERHKEPKELDSASSDEENEDGDFTVYECPGLAPTGEMEVRNPL
          SL.R.KE.K.LDSASSD.ENEDG.FTVYE.P.LA.TGEMEV..PL
Retrocopy SLKRDKEFKKLDSASSD-ENEDGNFTVYEGPDLALTGEMEVHTPL

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_1858 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	ENSOGAG00000002689	1 retrocopy	retro_ogar_1858 ,