RetrogeneDB ID: retro_ogar_635

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873524.1:33403612..33404345(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000027982
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NFKBIE
• Ensembl ID: ENSOGAG00000028890
• Aliases: None
• Description: nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon [Source:HGNC Symbol;Acc:7799]

Sequence

>retro_ogar_635
CCACAGGGACACTGAGCCCTCACTTACATCTCTGAGGACCGAGACACCCGGTCCACCTGGCAGGGATGCATGAGGCCCCA
GCAGTGGTGCTCTACTGTCTGGCTTTGCTGCCCCAGGAGGTCCTGGATATTCAGAATAACCTTTATCAGACAGCACTCCA
CCTGGCTGTACATCTGGACCAGCTGGGTGCAGTTTGGGCACTGGTGATGGAGAGGGCCAGTCGGGTGCTATGTCGGCATG
GTGCCAAGCCCTGCACGAGGCCTGCCAGCGCCAGCACCTGGCCTGTGCCCACTGCGTGCTAGAGGGGCAACCAGAGCCAG
GCAGAGGACCATCTCACTCCCTGGACCTCCAACTGCAAAACTGGCAAGATCTGACCTATCTCCACATCGCCACCCTGAAG
AGGAACCAGCTACTCATGGGACTACTGCTTCAGAATGGAGCTGATACTGATGCACTGGAGGGCACCAGTGGGAACACCGC
ATTGTCCCAGGCGGTGGAAACCCAGGCGCGAGGCCTGGTGCAGTTCCTGCTCCAGTCTGGAGCCCAGGTAGAAGCCTGCA
TTCTGAACGGGTGCACTCTCCTGCACCTGGGGGCTGGCCGGGGCCTCAGTGGCGTCTCATACATTGTGTGCAAGGCAGGT
GCTGACTCCTTGCTACGAAATGTGGAAGATGAGATACCCCAGCACCTGACTGAGGAACCCCTTGTTCTCTTGCCTTTTGA
TGACTTGAAGATC

Alignment

ORF - retro_ogar_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 67.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PQQLEALTYISEDGDTL-VHLAVIHEAPAVLLCCLALLPQEVLDIQNNLYQTALHLAVHLDQLGAVQALV
          PQ...ALTYISED.DT..VHLA..HEAPAV.L.CLALLPQEVLDIQNNLYQTALHLAVHLDQLGAV.ALV
Retrocopy PQGH*ALTYISEDRDTR<VHLAGMHEAPAVVLYCLALLPQEVLDIQNNLYQTALHLAVHLDQLGAVWALV

Parental  MKGASRVLQDRHGDT-ALHVACQRQHLACARCLLEAQPEPGRGPSHSLDLQLQNWQGLTCLHIATLKRNQ
          M..ASRVL..RHG...ALH.ACQRQHLACA.C.LE.QPEPGRGPSHSLDLQLQNWQ.LT.LHIATLKRNQ
Retrocopy MERASRVLC-RHGAK<ALHEACQRQHLACAHCVLEGQPEPGRGPSHSLDLQLQNWQDLTYLHIATLKRNQ

Parental  PLMELLLQNGADIDAQEGTSGKTALHLAVETQERGLVQFLLQSGARVDARMLNGCTPLHLAAGRGLSGIS
          .LM.LLLQNGAD.DA.EGTSG.TAL..AVETQ.RGLVQFLLQSGA.V.A..LNGCT.LHL.AGRGLSG.S
Retrocopy LLMGLLLQNGADTDALEGTSGNTALSQAVETQARGLVQFLLQSGAQVEACILNGCTLLHLGAGRGLSGVS

Parental  STLCKAGADSLLRNVEDETPQDLTEEPLVLLPFDDLKI
          ...CKAGADSLLRNVEDE.PQ.LTEEPLVLLPFDDLKI
Retrocopy YIVCKAGADSLLRNVEDEIPQHLTEEPLVLLPFDDLKI

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_635 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	ENSOGAG00000028890	1 retrocopy	retro_ogar_635 ,