RetrogeneDB ID: retro_ogar_1402

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873545.1:1516161..1517321(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033448
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IK
• Ensembl ID: ENSOGAG00000014281
• Aliases: None
• Description: IK cytokine, down-regulator of HLA II [Source:HGNC Symbol;Acc:5958]

Sequence

>retro_ogar_1402
ATGCCGGAGTGAGACAGTGAGCCATTTTCTAATCCTTTGGCCCCAGATGGCCATAATGTGGATGATCTTGCTCCTTTCAC
CAATCAAAACTCACCAAAGAAGACTTCAGGAAACTTCTCATGATGCCAAGGGCTGCACCTACTTCTGCACCACCTTCTAA
GTCACGTCATCATGAGATTCCAAGAGAATACAATGAGGATGAAGATCTAGCTGCAAGGAGGAGGAAAAAGAAAAGTTACT
ATGCCATGTTGTGTCAATAAGAAATTGAGAGAGAGAGAGCTAGCAGAGAAATACGGGACTGTGCCAAGGAACACAGAGAC
AGTGTGAACAAAGATTATGAGGAAACTGAGCTCATCAACACCACAACTAACTACAGAGCTGTGGGCCCCACTGCTGAGGA
GGACAAATCAGCCACAGAAAAGAGAAGACAATTGATCCAGGATTCCATATTCTTGGTTGGTGATATGGAACACACCTATT
TGGTGAAAGGCTTGGATATTGCTCTGCTTCAGAAGGTATGAGCTGAGATTGCCAGCAAAGAAAAAGAGGAAGAGGAACTG
ATGGAAAACCCCAGAAGGAAACCAAGAAAGATGAAGATCTTGAAAATAAAATTGAATTTAAAACACATCTGGGGCTCAAT
GTTTACCATATGCTTGCTTTTCAAGAGCAAAGCTTATGAGTAGAATGAGCTATTTCTGCCAGGCCCCATGGCCTATGTGG
TAGACCTGGATGATGAATATGCTGACATGGATATCCCCACCACTCTTATCTGTGGCAAGGCTGATTGTCCTACCATGGAA
GGCCAGACCATACTGACCACAAATGACATTGTCATCAGCAAGCTCACCCAGATCCTTTCATACCTGAGGCAGGATACTCA
CAATAAGAAGCTCAAGAAGAAGGATAAAGGGAAACTGGAAGAAAAGAAACCTCCTGAAGCTGCCATGAACATTTTTGAAG
ACATTGGGGATTACATTCCCTCCACGACCAAGACATCTAGGGACAAGGAGTGTGACAGATATCGGGAACGGGAGTGTGAT
TGGGAGAGAGACAGAGACTGTGACCAAAAGCAGGAACGAGAACCAGAGCGGGACACAGAGGGAGAAGAGGAAAAGAAGAG
GCACAGCTACTTTGAGAAGCCAAAAGTAGACGATGAGCCC

Alignment

ORF - retro_ogar_1402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 69.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPERDSEPFSNPLAPDGHDVDD-PHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDED
          MPE.DSEPFSNPLAPDGH.VDD...SFHQSKLT.EDFRKLLM.PRAAPTSAPPSKSRHHE.PREYNEDED
Retrocopy MPE*DSEPFSNPLAPDGHNVDD<SCSFHQSKLTKEDFRKLLMMPRAAPTSAPPSKSRHHEIPREYNEDED

Parental  PAARRRKKKSYYAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADKSA
          .AARRRKKKSYYA.L.Q.EIERER......RD.AKE.RD.VNKDYEETELI.TT.NYRAVGPTAE.DKSA
Retrocopy LAARRRKKKSYYAMLCQ*EIERER-ASREIRDCAKEHRDSVNKDYEETELINTTTNYRAVGPTAEEDKSA

Parental  AEKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELME-KPQKETKKDEDPENKIEF
          .EKRRQLIQ.S.FL.GDMEHT.LVKGLD.ALLQKV.AEIASKEKEEEELME.KPQKETKKDED.ENKIEF
Retrocopy TEKRRQLIQDSIFLVGDMEHTYLVKGLDIALLQKV*AEIASKEKEEEELME<KPQKETKKDEDLENKIEF

Parental  KTRLGRNVYRML-FKSK-AYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTND
          KT.LG.NVY.ML.F....AYE.NELFLPG.MAYVVDLDDEYAD.DIPTTLI..KADCPTME.QT.LTTND
Retrocopy KTHLGLNVYHMLAFQEQ>AYE*NELFLPGPMAYVVDLDDEYADMDIPTTLICGKADCPTMEGQTILTTND

Parental  IVISKLTQILSYLRQGTRNKKLKKKDKGKLEEKKPPEADMNIFEDIGDYVPSTTKTPRDKERERYRDRER
          IVISKLTQILSYLRQ.T.NKKLKKKDKGKLEEKKPPEA.MNIFEDIGDY.PSTTKT.RDKE..RYR.RE.
Retrocopy IVISKLTQILSYLRQDTHNKKLKKKDKGKLEEKKPPEAAMNIFEDIGDYIPSTTKTSRDKECDRYREREC

Parental  DRERDRDRDRERERERDRERERERDREREEEKKRHSYFEKP
          D.ERDRD.D...ERE..R..E.E....R............P
Retrocopy DWERDRDCDQKQEREPERDTEGEEEKKRHSYFEKPKVDDEP

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_1402 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618, retro_dnov_714, retro_dnov_960,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402 ,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419, retro_sara_558,