RetrogeneDB ID: retro_ogar_2104

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873591.1:2924969..2926141(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LAMP1
• Ensembl ID: ENSOGAG00000009899
• Aliases: None
• Description: lysosomal-associated membrane protein 1 [Source:HGNC Symbol;Acc:6499]

Sequence

>retro_ogar_2104
CTGCTGCTGCTCGGCCTCCCGCACAGTGCACTGGCAGTGTCCGTGGTGAGACATGGCAACGGGACAGCTTGTAGAATGGC
TCACTCCTCAGCTGCCTTCCTGATGAACTGTGACACTAAGAGTCGGTCTAAAAGTGTGACCTTTGACCTGCTACCAACTG
CAGAAGTGTTAAACAGCAGCTCTGGTGGTAAAGAGAACACTTCTGACTCCCCTTTCATGATTGCTTTTGGAGGAGGACAT
AGGCTGACTTTCAATTTCACAAGGGAGGCAGTGCGCTCCGGTGTCCAGCTCCTGCGTTCGGTGTATAACTTGTCACACAC
ACATATTTTCCCCATTGCAAGCTTCAAGGATGTCAAGACTGTGGAGTCCATAACTGACATCAAGGCAGATATAGATTAAA
AAATGCAGATGTGTTAAAGGCACCCAGGTGCACGTGGGCAATGTGATCGTCAGTCTCCGCGAGGCCACCATCTAGGCATA
GCTTTTAAACAACAGCTTCAGCAAGGGAGAGATGCCTTGGAAGCAGGATGGGCCTTTCTCCACCACAGCGCCACTTATGC
CTCCCAGCCCCTCTCTGTTGCCAATACCAGAGAGTCCCTCAGTGGAAAAGTACAATGTGAGCTGCAGCAACGGGACCTGC
CTCCTGGCCAGCAAGGAGCTGCGGCTGATCCTCACCTACGAGAGGAGGGACAACATGAACGTGACTCCAAGGTCAACCTG
AACAACACCGAGGTCAACAGGGATTTGCAGCTGCAGCCTAGTGACCCTGGACCTGCGGAGCAAGATCGCTCTCCTGGTCT
TCCAGTTTGGGATGAGTGCAAATTCTAGCTGGTTTTTTCCTGCGAGGAATCCAGTTAAATGTGATTCTTGCTGATGCTCC
AGATCCCCTTTCAGAACTTCGAATGACTCGCTCCTGGCGCTGCAGGCCACCCTGGGAAATTCCTGTAAGTGCAATGTCCA
GCAGCCGTTCAGGTCACAAAGGCACTTTCTGTCAACATCTTCAAAGTCTGGGTCCAGTCCTTCAAAATGGAAGGCAGCAA
GTTTGCATCTGTAGAAGAGTGTCTGCTGGACGAGGACAGCATGCAGATTCCCGTGACCATGGGGGCGCCCTGGCCAGGCT
GGTCCTCATGGCTCTAATCGCCTACCTCATGTTGTTCAGAAGAGGAGCTGCA

Alignment

ORF - retro_ogar_2104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.92 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LELAGLLHGALAVFVVKNGNGTACIMAEFSAAFQMNYDTKSGPKNVSFDLPPTAKVLNSSSCGKENTSDT
          L.L.GL.H.ALAV.VV..GNGTAC.MA..SAAF.MN.DTKS..K.V.FDL.PTA.VLNSSS.GKENTSD.
Retrocopy LLLLGLPHSALAVSVVRHGNGTACRMAHSSAAFLMNCDTKSRSKSVTFDLLPTAEVLNSSSGGKENTSDS

Parental  RLVIAFGGGHELTFNFTRDADRYSVQLLSFVYNLSDTLIFPNASFKDAKTVESITDIKADID-KKYRCVK
          ...IAFGGGH.LTFNFTR.A.R..VQLL..VYNLS.T.IFP.ASFKD.KTVESITDIKADID.KK.RCVK
Retrocopy PFMIAFGGGHRLTFNFTREAVRSGVQLLRSVYNLSHTHIFPIASFKDVKTVESITDIKADID>KKCRCVK

Parental  GTQVHMGNVSLTLREATIQAYLSNNNFSKGETRCKQDGPFPTTVPPVPPSPS--PAPESPSVENYSVNGT
          GTQVH.GNV...LREATI.A.L.NN.FSKGE...KQDGPF.TT.P..PPSPS..P.PESPSVE.Y.V...
Retrocopy GTQVHVGNVIVSLREATI*A*LLNNSFSKGEMPWKQDGPFSTTAPLMPPSPSLLPIPESPSVEKYNVSCS

Parental  NGTCLLASMGLQLNLTYEQRDNKTVTRVFNINPSKTWANGTCSSNLVTLDLWSEDVARLVFQFGMNANST
          NGTCLLAS..L.L.LTYE.RDN..VT...............CS..LVTLDL.S...A.LVFQFGM.ANS.
Retrocopy NGTCLLASKELRLILTYERRDNMNVTPRST*TTPRSTGICSCS--LVTLDLRSK-IALLVFQFGMSANSS

Parental  -RFFLQDIQLSMILADARDP-HFTASNGSLMALQATLGNSYKCNAEE-RIQVTKAFSVNIFKVWVQAFKV
          ..FFL..IQL..ILADA.DP..F..SN.SL.ALQATLGNS.KCN......QVTKA.SVNIFKVWVQ.FK.
Retrocopy >GFFLRGIQLNVILADAPDP<PFRTSNDSLLALQATLGNSCKCNVQQ<AVQVTKALSVNIFKVWVQSFKM

Parental  EGGKFGSVEECLLDEDSMLIPVAV-GGALAGLVLTVLIAYLVGRKRSHA
          EG.KF.SVEECLLDEDSM.IPV...GGALA.LVL..LIAYL....R..A
Retrocopy EGSKFASVEECLLDEDSMQIPVTM<GGALARLVLMALIAYLMLFRRGAA

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_2104 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
Equus caballus	ENSECAG00000017618	1 retrocopy	retro_ecab_1056,
Otolemur garnettii	ENSOGAG00000009899	1 retrocopy	retro_ogar_2104 ,
Tursiops truncatus	ENSTTRG00000004460	1 retrocopy	retro_ttru_1542,