RetrogeneDB ID: retro_ogar_2043

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873584.1:9085666..9086715(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030383
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3H
• Ensembl ID: ENSOGAG00000008905
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit H [Source:HGNC Symbol;Acc:3273]

Sequence

>retro_ogar_2043
AAGGAAGGCACTGGCTCTACCGCTGCCTCTTCTACCTTTACCACCAGCACTGCAGGGAAAGACAAGGGCAAAGGCAGCTC
TGGAGATTTGGCTGTGAAGCAAGTGCAGAGAGATGGGTTGGTGGTATTAAAGATAATCAAACATTACCAAGAAGAAGGAC
AAGGAACTGAAGTTGTTTGGGAGGTGCTTTGGGGTCTGGTTGGAAAAGGTCAGCTTGAAGTTACCAACTGCTTTCCCTTC
CCTCAACACACAGAGGATGATACAGACTTTGATGAAGTCCAGCACCAGATGGAAATGATGCGGAGCCTTTGCCATATAAA
CATCGATCATCTTTACATGGGCTGGTACCAGTCCACGTACTGTGGCTCATTCGTCACCCGGGCACTCCTAGATTCTCAGT
TCAGTTACCAACATGCCATTGAAGAATCTGCCGGTCTCATTTATGATCCCATAAAAACTGCCCCAGGGTCTCTTTCACTG
AAAGCATACAGACTGACTCTTAAACTGATGGAAGTTTGTAAAGAGAAGGATTTTTCCCCTGAGGCATTGAAAAAAGCAAA
TATCATCTTTGAGCTCATGTTTGACGAAGTGCTGATTGTAATTAAAAATTCACATCTGGTCAACATCCTAATGTGGGAAC
TTGAAAAGAAGTCAGCTGTAGCAGATAAACATGAATTGCTCAGCCTTGCTAGCTGCAATCATTTGGGGAAGAATCCCAGT
TGCTCACAGACAGAGTGGATGATATGAGCCAAGATATAGTTAAATATAACATATGAGGAACACTAGTAAACAGCAGCACC
AGAAATATCAGTATCAACAATGTTGCCAACAGGAGAACATGCAGCGTCAGAGCCGAGGGGAACCCCCACTCCCTGAGGAG
GATCTGTCCAAACTCTTCAAACCGCTGCAGCCCCCTGACAGGATGGACTCCCTGCTCATCGCAAGCTAGATTAATACTTA
CTGATGTTGCTGCCAGAATATCAAGGAAATCACTGCCCCCAAACTTAGGCAAACTCTTCATGGCCCAGGCCCTTCAAGAA
TACAATAAT

Alignment

ORF - retro_ogar_2043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.49 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KEGAGSTATSSSSTTGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGLVVED
          KEG.GSTA.SS..TT..AGK.KGKG.SGD.AVKQVQ.DGLVVLKIIKHYQEEGQGTEVV..VL.GLV...
Retrocopy KEGTGSTAASSTFTTSTAGKDKGKGSSGDLAVKQVQRDGLVVLKIIKHYQEEGQGTEVVWEVLWGLVGKG

Parental  RLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFSYQHAI
          .LE.TNCFPFPQHTEDD.DFDEVQ.QMEMMRSL.H.NIDHL..GWYQSTY.GSFVTRALLDSQFSYQHAI
Retrocopy QLEVTNCFPFPQHTEDDTDFDEVQHQMEMMRSLCHINIDHLYMGWYQSTYCGSFVTRALLDSQFSYQHAI

Parental  EESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEHMFEEVPIVIKNSHLINVL
          EES..LIYDPIKTA.GSLSLKAYRLT.KLMEVCKEKDFSPEALKKANI.FE.MF.EV.IVIKNSHL.N.L
Retrocopy EESAGLIYDPIKTAPGSLSLKAYRLTLKLMEVCKEKDFSPEALKKANIIFELMFDEVLIVIKNSHLVNIL

Parental  MWELEKKSAVADKHELLSLASSNHLGKN-LQLLMDRVDDMSQDIVKYNT-YMRNTSKQQQQKHQYQQRRQ
          MWELEKKSAVADKHELLSLAS.NHLGKN..QLL.DRVDDMSQDIVKYN.........Q.Q.K.QYQQ..Q
Retrocopy MWELEKKSAVADKHELLSLASCNHLGKN<SQLLTDRVDDMSQDIVKYNI<MRNTSKQQHQ-KYQYQQCCQ

Parental  QENMQRQSRGEPPLPEEDLSKLFKPLQPPARMDSLLIAGQINTY---CQNIKEFTA-QNLGKLFMAQALQ
          QENMQRQSRGEPPLPEEDLSKLFKPLQPP.RMDSLLIA..INTY...CQNIKE.TA..NLGKLFMAQALQ
Retrocopy QENMQRQSRGEPPLPEEDLSKLFKPLQPPDRMDSLLIAS*INTY*CCCQNIKEITA>PNLGKLFMAQALQ

Parental  EYNN
          EYNN
Retrocopy EYNN

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_2043 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043 ,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,