RetrogeneDB ID: retro_ogar_2228

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873604.1:8585917..8586969(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUPL1
• Ensembl ID: ENSOGAG00000003821
• Aliases: None
• Description: nucleoporin like 1 [Source:HGNC Symbol;Acc:20261]

Sequence

>retro_ogar_2228
GTCCTCCAGGATGTGGAAAATCTCCAGAAATTTGTGAAGGAACAAAAACAAGTCCAAGAAGAAATTAAGAGAATGTGGTC
CAAAGCAATGCTTCAAGTACAAGAAGATATCAAAGCTCTAAACCAGCTTCTGTCCTTGGCTACCAGGGGACTACAGAGAA
ACACTCTCTGTATTGACAAATTGAAAATAGAAACTGCTCAGGGATTAAAGAGCGCTGAAATAGCTTTAAGGACCCAGAAA
TCACCACCTGGACTTCAACGTGAAAATACAGCTCGTGCAGACTCCTTCAGAATGTTGGTTCAATAATTTGAGGTACAACT
TCAGTAGGACAGACTTCAACAGATTGAAGAACTAGAAAATCATCCTGCCACTCAAGCAAATAATTCACGTATAACCCCAC
AAGATTTGTCGATGGCTTTGCAGAAAATTTATCAAACATTCGTAGCTTTAGCTGCACAGCTTCCGTCTATTCAGGAAAAT
GTAAAGGTGCTCAAAGATGAGCACCCTGGCTACAGGAGAATGTTCCTGGGAGACGCTGGAGATGTGTTTGGAGCCAGGTG
AGCAGAAGCTAAGAAGCGGCAGAATGCACCCCGAGTCTAGCACACCCACTAGACCCACAGCTTTCAGCACCAAGCCAAAC
ACAGCTGTTGCCATGGCTGCAACACTTACACAGTAGCAGCAGCCTGCCACAGGCCACCGCCGTCTCTGGGAGTTAGTTTT
GGAACGCCATTCAGCTAAGTATTGGCACTGGCTGGCGATTAAGTGGCTTGGGTTCTTCAAACCTTGGAGGATTTGGAACT
AGCTCTGGTTTTGGATGCAGCACCACAGGGGCCCCCACATTTTGATTTAGAACAACAAATAAACCCTCAGGAAGTCTCAG
TGCAAGCTTTGGCAGCTCAATTACATCTGGGTTTAACTTCAGTAATCCTGGCATCACGGCATCAGCTGGTTTGACATTCG
GGGTGTCCAATCCTGCCTCTGCGGGTTTGGGAACAGGAGGACAACTCCTTCAGGTGAAGAAACCTCCCACTGGAAACAAA
AGAAGGAAAAGA

Alignment

ORF - retro_ogar_2228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.68 %
• Parental protein coverage: 59.42 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IYQDVENLQKFVKEQKQVQEEISRMSSKAMLKVQEDIKALKQLLSLAASGLQRNTLNIDKLKIETAQELK
          ..QDVENLQKFVKEQKQVQEEI.RM.SKAML.VQEDIKAL.QLLSLA..GLQRNTL.IDKLKIETAQ.LK
Retrocopy VLQDVENLQKFVKEQKQVQEEIKRMWSKAMLQVQEDIKALNQLLSLATRGLQRNTLCIDKLKIETAQGLK

Parental  NAEIALRTQKTPPGLQHENTAPADYFRILVQQFEVQLQQYR-QQIEELENHLATQANNSHITPQDLSMAM
          .AEIALRTQK.PPGLQ.ENTA.AD.FR.LVQ.FEVQLQ..R.QQIEELENH.ATQANNS.ITPQDLSMA.
Retrocopy SAEIALRTQKSPPGLQRENTARADSFRMLVQ*FEVQLQ*DRLQQIEELENHPATQANNSRITPQDLSMAL

Parental  QKIYQTFVALAAQLQSIHENVKVLKEQYLGYRKMFLGDAVDVFEARRAEAKKWQNAPRV-TTGPTPFSTM
          QKIYQTFVALAAQL.SI.ENVKVLK....GYR.MFLGDA.DVF.AR.AEAKK.QNAPRV..T...P....
Retrocopy QKIYQTFVALAAQLPSIQENVKVLKDEHPGYRRMFLGDAGDVFGAR*AEAKKRQNAPRV>STPTRPTAFS

Parental  PNAAAVAMAATLTQQQQPATAG-PQPSLGVSFGTPFG-SGIGTGLQSSGLGSSNLGGFGTSSGFGCSTTG
          .........A....Q.Q....G.P.PSLGVSFGTPF....IGTG...SGLGSSNLGGFGTSSGFGCSTTG
Retrocopy TKPNTAVAMAATLTQ*QQPATG<PPPSLGVSFGTPFS<LSIGTGWRLSGLGSSNLGGFGTSSGFGCSTTG

Parental  ASTFGFGTTNKPSGSLSAGFGSSSTSGFNFSNPGITASAGLTFGVSNPASAGFGTGGQLLQLKKPPAGNK
          A.TF.F.TTNKPSGSLSA.FGSS.TSGFNFSNPGITASAGLTFGVSNPASAG.GTGGQLLQ.KKPP.GNK
Retrocopy APTF*FRTTNKPSGSLSASFGSSITSGFNFSNPGITASAGLTFGVSNPASAGLGTGGQLLQVKKPPTGNK

Parental  RGKR
          R.KR
Retrocopy RRKR

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_2228 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	ENSOGAG00000003821	1 retrocopy	retro_ogar_2228 ,