RetrogeneDB ID: retro_ogar_3118

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873721.1:476458..477175(+)
• Located in intron of: ENSOGAG00000009684

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM184C
• Ensembl ID: ENSOGAG00000015819
• Aliases: None
• Description: transmembrane protein 184C [Source:HGNC Symbol;Acc:25587]

Sequence

>retro_ogar_3118
TTATCTAACCAGTATCCAAATCTGGGATTAATTCTTAAAGTTAAAGATCAGCAGAAACATTTTCCTTCTTTATGTTGCTG
TCCACCACGAGCTATGGGAGAAGTATTGCTGTTTAGGTGCAAACTAGGTGTATCACAATATACAGTTGTCAGACCATTCA
ACACCATTGTTGCTTTAATTTATGAGCTGCTTGGTATATATGACTTTAGCTTTTCAAATGCTTGGACTTGAATTTGGTTA
TAATAAACAATGTGTTACAACTGTCTGCCATATATTGTCTCTTGCTATTTTATAAAGTTATAAAAGAAGAACTGAGTCCA
ATCCAACCTGTTGGAAAATTTCTTTGTGTAAAGCTGGTGGTTTTTGTTTCTTTTTGGCAAGCAGTAGTTATTGCTTTGTT
GGTAAAAGTTGGTGTTATTTCTGAAAAGCATTCATGGGCATGGCAAACTGTAGAAGCTGTGGCTACAGGACTCCAGGACT
TTATAATCTGTACTGAGATGTTCCTTATTGCTATTGCTTATCACAACACTTTCTCATATAAACCATGTGTCCAAGAAACA
GAAGAGGGCTCATGCTTTAGTCTTTTCTTGCCATGTGGGATGTTTCAGATATTAGAGATGATATATCTAAACAAGGAAGG
CATGTTGTTGGATGGACAGTCGGGGACATCCTAGGAAAAAACTGTTTCCCAAGGATCAAGATCAAAATGAATATACG

Alignment

ORF - retro_ogar_3118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.11 %
• Parental protein coverage: 55.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTNRYPNLVLILEAKDQQKHFPPLCCCPPWAMGEVLLFRCKLGVLQYTVVRPFTTIVALICELVGIYDEG
          L.N.YPNL.LIL..KDQQKHFP.LCCCPP.AMGEVLLFRCKLGV.QYTVVRPF.TIVALI.EL.GIYD..
Retrocopy LSNQYPNLGLILKVKDQQKHFPSLCCCPPRAMGEVLLFRCKLGVSQYTVVRPFNTIVALIYELLGIYD--

Parental  NFSFSNAWTYL-VIINN-MSQLFAMYCLLLFYKVLKEELSPIQPVGKFLCVKLVVFVSFWQAVVIALLVK
          .FSFSNAWT.....I.N...QL.A.YCLLLFYKV.KEELSPIQPVGKFLCVKLVVFVSFWQAVVIALLVK
Retrocopy -FSFSNAWT*I<LVIINNVLQLSAIYCLLLFYKVIKEELSPIQPVGKFLCVKLVVFVSFWQAVVIALLVK

Parental  VGVISEKHTWEWQTVEAVATGLQDFIICIEMFLAAIAHHYTFSYKPYVQEAEEGSCFD-SFLAMWDVSDI
          VGVISEKH.W.WQTVEAVATGLQDFIIC.EMFL.AIA.H.TFSYKP.VQE.EEGSCF..SFLAMWDVSDI
Retrocopy VGVISEKHSWAWQTVEAVATGLQDFIICTEMFLIAIAYHNTFSYKPCVQETEEGSCFS<SFLAMWDVSDI

Parental  RDDISEQVRH-VGRTV-RGHPRKKLFREDQDQNEHT
          RDDIS.Q.RH.VG.TV.RGHPRKKLF..DQDQNE.T
Retrocopy RDDISKQGRHVVGWTV<RGHPRKKLFPKDQDQNEYT

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_3118 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002418	1 retrocopy	retro_cjac_2276,
Felis catus	ENSFCAG00000015410	2 retrocopies	retro_fcat_1929, retro_fcat_755,
Homo sapiens	ENSG00000164168	1 retrocopy	retro_hsap_4870,
Macaca mulatta	ENSMMUG00000004977	1 retrocopy	retro_mmul_2611,
Otolemur garnettii	ENSOGAG00000015819	1 retrocopy	retro_ogar_3118 ,
Tarsius syrichta	ENSTSYG00000005633	1 retrocopy	retro_tsyr_1001,