RetrogeneDB ID: retro_ogar_1210

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873539.1:15869607..15871062(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000026814
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000034779
• Aliases: None
• Description: None

Sequence

>retro_ogar_1210
ATGTGCAATACCAACATGTCTGTGTCTACTGATGTAACCACCTCACAGATTCCAGCTTCGGAACAGGAGACCCCGGTTAA
ACCAAAACCATTGCTTTTTAAGTTGTTAAAGTCTGTTGGTACACAAAAAGACACTTACACAATGAAAGAGGTTATATTTT
ATCTTGGCCAGTGTATTATGACGAAACGATTATATGATGAAAAGCAACAACATATGTATATTGTTCAAATGATCTTCTAG
GAGATTTGTTTGGAGTGCCAAGCTTCTCTGTGAAAGAGCACAGGAAGATATATACAATGATCTACAGAAACTTGGTAGTA
GTCAATCAGCAGGAATTATCAGACTCAGGTACATCTGTGAGTGAGAACAAATGTCACCTTGAAGATGGGAGTGATCAGAA
GGATCCTGTGCCAGAGAAACCTTCCTCTTCAAATTGGGTTTCCAGATCATCTACCTCATCCAGAAGGAGAGCCATCAGTG
AGACAGAAGAAAATTCAGATGAATTGTCTGGAGAAGGACAGAGAAAATGGCATAGAGCTGATAGTATTTCCCTGTCCTTT
GATGAAAGCCTGGCTCTGTGTGTGATCAGGGAGATCTGCTGTGAAAGAAGCAGCCCCAGTGAGTCTCCAGGGACACCGCC
TCACCCGGATCTTGATGCTGGTGTAAGTGAACATTCAGGTGACTGGTTGGATCAGGATTCAGTTTCAGATCAGTTTAGTG
TAGAATTTGAAGTTGAATCTCTTGATTCGGAAGATTATAGTCTTAGTGAAGAAGGACAAGAACTCTCAGATGAAGATGAT
GAGGTGTATCAAGTTACTGTGTCTCAAGCAGAGGAGAGTGATACAGATTCATTTGAAGAAGATCCTGAAATTTCCCTAGC
TGACTATTGGAAAAGTACTTCATGCAATGAAATGAATCCTCCCCTTCCACCACATTGCAAAAGATGTTGGACCTTTCGTG
ACAATTGGCTTCCTGAAGATAAAGGAAAAGACAGAAGGGATATCTCTGAGAAAGCCAAACTAGAAAACTCAGCACAAGCC
GAAGAGGGCTTTGATGTTCCGGATTGTAAAAAAAACTACAGGGAGTGATTCCAAAGAGTCATCTGTGGAGGAAAATGATG
ATAAAATCACTCAGGCCTCCCAGTCACAAGACAGTGAGGACTATTCTCAGCCATCAACTTCTAACAGCATTATTTACAGC
AGCCAAGAAGATGTCAAAGAGTTTGAGAGGGAGGAAACCCAAGACAAAGAAGAGAGTATGGAATCCAGCTTTCCCCTTAA
TGCCATTGAACCTTGTGGGATTGGCCAAGGTCGACCTAAAAATGGTTGCACTGTCCATGGTAAAACAGGACATCTTATGG
CATGCTTCACATGTGCAAAGAAGCTGAAGAAGAGGAACAAGCCCTGCCCAGTGTGCAGACAGCCGATCCAGATGATCGTG
CTAACGTACTTCCCC

Alignment

ORF - retro_ogar_1210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCNTNMSVSTDVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVIFYLGQYIMTKRLYDEKQQ
          MCNTNMSVSTDVTTSQIPASEQET.V.PKPLL.KLLKSVG.QKDTYTMKEVIFYLGQ.IMTKRLYDEKQQ
Retrocopy MCNTNMSVSTDVTTSQIPASEQETPVKPKPLLFKLLKSVGTQKDTYTMKEVIFYLGQCIMTKRLYDEKQQ

Parental  HI-VYCSNDLLGDLFGVPSFSVKEHSPTRKIYTMIYRNLVVVNQQELSDSGTSVSENKCHLEDGSDQKDP
          H..VYCSNDLLGDLFGVPSFSVKEH...RKIYTMIYRNLVVVNQQELSDSGTSVSENKCHLEDGSDQKDP
Retrocopy HM<VYCSNDLLGDLFGVPSFSVKEH---RKIYTMIYRNLVVVNQQELSDSGTSVSENKCHLEDGSDQKDP

Parental  VPELQEEKPSSSNWVSRPSTSSRRRAISETAQIPRDAFSRMAFRKHSDFLISIEIIQSFAARLRRELQLC
          VP....EKPSSSNWVSR.STSSRRRAISET...............H....IS.....S.A....RE...C
Retrocopy VP----EKPSSSNWVSRSSTSSRRRAISETEENSDELSGEGQRKWHRADSISLSFDESLALCVIREI-CC

Parental  SESVCPRSSERPGQPDLDAGVSEHSGDWLDQDSVSDQFSVEFEVESLDSEDYSLSEEGQELSDEDDEVYR
          ..S....S...P..PDLDAGVSEHSGDWLDQDSVSDQFSVEFEVESLDSEDYSLSEEGQELSDEDDEVY.
Retrocopy ERSSPSESPGTPPHPDLDAGVSEHSGDWLDQDSVSDQFSVEFEVESLDSEDYSLSEEGQELSDEDDEVYQ

Parental  VTVYQAEESDTDSFEEDPEISLADYWKCTSCNEMNPPLPSHCNRCWTLRENWLPEDKGKDRRDISEKAKL
          VTV.QAEESDTDSFEEDPEISLADYWK.TSCNEMNPPLP.HC.RCWT.R.NWLPEDKGKDRRDISEKAKL
Retrocopy VTVSQAEESDTDSFEEDPEISLADYWKSTSCNEMNPPLPPHCKRCWTFRDNWLPEDKGKDRRDISEKAKL

Parental  ENSAQAEEGFDVPDC-KKTTGSDSKESSVEVNDDKITQASQSQDSEDYSQPSTSNSIIYSSQEDVKEFER
          ENSAQAEEGFDVPDC....TGSDSKESSVE.NDDKITQASQSQDSEDYSQPSTSNSIIYSSQEDVKEFER
Retrocopy ENSAQAEEGFDVPDC>XXXTGSDSKESSVEENDDKITQASQSQDSEDYSQPSTSNSIIYSSQEDVKEFER

Parental  EETQDKEESLESSFPLSAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIV
          EETQDKEES.ESSFPL.AIEPC.I.QGRPKNGC.VHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIV
Retrocopy EETQDKEESMESSFPLNAIEPCGIGQGRPKNGCTVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIV

Parental  LTYFP
          LTYFP
Retrocopy LTYFP

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_1210 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004323	1 retrocopy	retro_cpor_1234,
Loxodonta africana	ENSLAFG00000005885	1 retrocopy	retro_lafr_715,
Otolemur garnettii	ENSOGAG00000011679	1 retrocopy	retro_ogar_1852,
Otolemur garnettii	ENSOGAG00000034779	2 retrocopies	retro_ogar_1210 , retro_ogar_49,
Ochotona princeps	ENSOPRG00000009677	1 retrocopy	retro_opri_891,
Ictidomys tridecemlineatus	ENSSTOG00000014702	1 retrocopy	retro_itri_1731,
Tupaia belangeri	ENSTBEG00000013758	2 retrocopies	retro_tbel_3216, retro_tbel_915,
Tarsius syrichta	ENSTSYG00000002908	2 retrocopies	retro_tsyr_1343, retro_tsyr_984,