RetrogeneDB ID: retro_ogar_1227

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873539.1:8235289..8235777(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000024224
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSOGAG00000004694
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit J [Source:HGNC Symbol;Acc:3270]

Sequence

>retro_ogar_1227
AAAAAGAGGTTGGAAGAACCTGAAGAACCTAAAGTGCTAACACCGGAAGAACAATTAGCAGATAAACTGCAGTTAAAGAA
ATTGCAGGAAGAGTCAGACCTTGAATTAGCAAAGGAAACTTTCGGTGTTAATAATACAGTTTTTGGAATAGATGCTATGA
ACCCATCTTCAAGAGATGACTTCACAGAATTTGGAAGGTTACTAAAAGATAAAATTACACAATATGAAAAGTCACTATAT
TATGCTAGTTTTTTGGAAGTCTTAGTTCGAGATGTGTGTATTTCATTGGAAATTGATGACTTGAAAAAGATTACCAATTC
ATTGACTGTCCTTTGCAGTGAAAAACAGAAGCAAGAAAAGCAAAACAAAGCCAAAAAGAAGAAGAAAGGTGTGGTTCCTG
GAGGGGGATTAAAGGCACCATGAAAGACGATCTGGCAGATTATGGTGGTTATGATGGAGGATATGTACAAGACTATGAAG
ACTTCATG

Alignment

ORF - retro_ogar_1227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 61.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVFGIDAMNPSSRDDFTEFGRLLKD
          KKRLEEPEEPKVLTPEEQLADKL.LKKLQEESDLELAKETFGVNNTVFGIDAMNPSSRDDFTEFGRLLKD
Retrocopy KKRLEEPEEPKVLTPEEQLADKLQLKKLQEESDLELAKETFGVNNTVFGIDAMNPSSRDDFTEFGRLLKD

Parental  KITQYEKSLYYASFLEVLVRDVCISLEIDDLKKITNSLTVLCSEKQKQEKQNKAKKKKKGVVPGGGLKA-
          KITQYEKSLYYASFLEVLVRDVCISLEIDDLKKITNSLTVLCS...............KGVVPGGGLKA.
Retrocopy KITQYEKSLYYASFLEVLVRDVCISLEIDDLKKITNSLTVLCSXXXXXXXXXXXXXXXKGVVPGGGLKA<

Parental  TMKDDLADYGGYDGGYVQDYEDFM
          TMKDDLADYGGYDGGYVQDYEDFM
Retrocopy TMKDDLADYGGYDGGYVQDYEDFM

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_1227 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227 ,