RetrogeneDB ID: retro_ogar_816

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873528.1:734291..735464(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000032409
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LRRC42
• Ensembl ID: ENSOGAG00000016552
• Aliases: None
• Description: leucine rich repeat containing 42 [Source:HGNC Symbol;Acc:28792]

Sequence

>retro_ogar_816
ATGTCTTACTACTCAGAAAGCCACCTGGACTCAAGGCCCATCTACGTGCAAGAAAATGGGCAGCTGCACGTGGTCAATAG
GGCTCTGGATGATGTCAAGAGTGGCCTACAGAAACCAAGACCTGTCAGACTGTGTCCCAAAGGCTTTTCCGTGGAGCTAT
GCATGAATGGAGAAGATGATACTGCACAGAAAGAGAAGACTGATCATTTCATCTTCACGTATACCCGGGAAGGAAATCTT
CGGTACTCCCCCAAATCCCTCTTCAGCCTTATCCTGGGCTTCATCTCTGACAATGTTGATCAGATTGATTCCCTTGTTGG
CTTTCCTGAGCAGATTGCTGAAAAGCTGTTCTCTGAAGCTGAAGCCAGACAGAAATTCACAGAGCCAGGGGTGGGGCTGA
GGGCTTTACAGATATTCACTGAGGCCTATGGAAGTCTAGTGCTTTGCTCCTTGTGTTTGAGAAACAGGTATCTGGTGATT
TCAGAAAAACTTGAGGAGATTAAGTCTTTCCGGGATCTGACCTGCCTGGATCTTTCCTGTTGCAAGCTTGGAGATGAGCA
TGAACTTTTAGAACATCTCACCAGTGAAGCCCTGTCTACCATAACTCAACTCCACCTGAAGGATAATTGTTTATCTGATG
CTGGGGTACAGAAAATGACAGCACCAGTTAGAGTGATGAAAAGAGGCCTTGAAAATCTAGCATTATTAGACCTGTCATGT
AACCCTGAGATTACAGACGCAGGAATAAGATACCTCTTTTCTTTTAGAAAACTCAACTGCTTAGATATCTCTGGGACTGG
GCTTAAGGACATCAAAGCTGTCAAGCACGAGCTCCAGACTCACATAGGCCTTATTCACTCCAATGTGCCTTTGAAGGAAT
TTGATCATAGTAACTGCAAGACAGAGGGCTGGGCTGACCACATCATTCTGCAATGGGAGCGTATGACTGCGGAAGCTGCA
AAGCCACGGGAAACCTCAGAGCCACGAACAGCAGCTCAGCACTTCCATGGGAAGTGGGCTCAAGCAGAAGCTCCAGTGAA
GTGTCCTCCGGCAGACATCCACATAAACTCTTCAGAGAAACTACAGTTCTATAGAGAGAAAACCCTGGACTGCCATGGGA
CATTGTTGAAATGTGAAGCTGTCTCAAGCCAGGAGTCAACAGTGCAAAAAGAG

Alignment

ORF - retro_ogar_816 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.24 %
• Parental protein coverage: 91.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYYLNSESPLDPGPIYVRENGQLHMVDLALEGVRSGLQKPKPFRLFPKGFSVELCMNREEDTAHKEKTD
          MSYY..SES.LD..PIYV.ENGQLH.V..AL..V.SGLQKP.P.RL.PKGFSVELCMN.E.DTA.KEKTD
Retrocopy MSYY--SESHLDSRPIYVQENGQLHVVNRALDDVKSGLQKPRPVRLCPKGFSVELCMNGEDDTAQKEKTD

Parental  HFIFTYTREGNLRYSAKSLFSLVLGFISDNVDHIDSLIGFPEQIAEKLFSAAEARQKFTEPGAGLRALQK
          HFIFTYTREGNLRYS.KSLFSL.LGFISDNVD.IDSL.GFPEQIAEKLFS.AEARQKFTEPG.GLRALQ.
Retrocopy HFIFTYTREGNLRYSPKSLFSLILGFISDNVDQIDSLVGFPEQIAEKLFSEAEARQKFTEPGVGLRALQI

Parental  FTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFRELTCLDLSCCKLGDEHELLEHLTNEALSSVTQLHLKD
          FTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFR.LTCLDLSCCKLGDEHELLEHLT.EALS..TQLHLKD
Retrocopy FTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFRDLTCLDLSCCKLGDEHELLEHLTSEALSTITQLHLKD

Parental  NCLSDAGVRKMTAPVRVMKRGLENLTLLDLSCNPEITDAGIGYLFSFRKLNCLDISGTGLKDVKAVKHKL
          NCLSDAGV.KMTAPVRVMKRGLENL.LLDLSCNPEITDAGI.YLFSFRKLNCLDISGTGLKD.KAVKH.L
Retrocopy NCLSDAGVQKMTAPVRVMKRGLENLALLDLSCNPEITDAGIRYLFSFRKLNCLDISGTGLKDIKAVKHEL

Parental  QTHIGLVHSKVPLKEFDHSNCKTEGWADQIVLQWERVTAEATKLRENSQPRTAARHFYGKRAPAEAPVTC
          QTHIGL.HS.VPLKEFDHSNCKTEGWAD.I.LQWER.TAEA.K.RE.S.PRTAA.HF.GK.A.AEAPV.C
Retrocopy QTHIGLIHSNVPLKEFDHSNCKTEGWADHIILQWERMTAEAAKPRETSEPRTAAQHFHGKWAQAEAPVKC

Parental  PLADPHMNSSEKLQFYREKAPDCHGPLLKCEAVSSQESKKSKK
          P.AD.H.NSSEKLQFYREK..DCHG.LLKCEAVSSQES...K.
Retrocopy PPADIHINSSEKLQFYREKTLDCHGTLLKCEAVSSQESTVQKE

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_816 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016552	1 retrocopy	retro_ogar_816 ,
Ochotona princeps	ENSOPRG00000005566	1 retrocopy	retro_opri_15,
Ictidomys tridecemlineatus	ENSSTOG00000022786	1 retrocopy	retro_itri_1536,