RetrogeneDB ID: retro_ogar_296

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: AAQR03191848.1:5722..6671(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSOGAG00000007258
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_ogar_296
ATGGACCTAAAACTTAAAAATTGTGAGTTCTAGTATAGTCTCCATGGCCAGGTACCAGGGCTGCTGGATTGAGACATGGG
GAGTGAGTTATTTCTGCCTTGTACCACAGACCATTGACCCTTAGCTGAGCAGAACCTTACCAAATATAGACTCCGAGTAA
TGAAGCCTCCAAAGGTCCCTCAGGAGAAGAGACCCAGTCCTGATGAAGGTGGGCCACACTCTGAACCTATCCTGTGGATG
TGGGTGAACCCTAACATTGTGTGCCCCATCGGCAGCCAGGAGGTCCCAAAGCCTGGTGAAAAAAAAGATCTGATAAGCAT
GCCTCCTTCCTCTCAGCTACCTCTGAAGGATGAAGAGTCTAACTGCTCAGAGGCCACAGTGGTAGAGTCCCTGCTGTTTT
CCTCTGGTAAGCAGTCTCCCTTACAGAAGCAGTTCCACTCTTCCCCTAGTGACTGGGAACTCACAGAAGAGGAGACTGAA
GAACAAGATGACAGTTCTTCTGTGGCCTTCCAGCCTCCTAACAAAAAGAAGTGCTTTAAGAGCCAGAAGCTGTGGCAAGT
CAACAACCAGGAGAGGAGGTCCTGGCCATGGCCTCTTCTCAATTACAGCCACCTAATTGCACTAGCATTAAAAAATAGCC
ACCCCTGTGGCCTCAATGTGCAAGAGATCTACAATTTCACCCAACAGCATTTCCCCTTTTTCTGGACAGCTCCAGATGGC
TGGAAGAACACCATTTACCATAATCTTTGCTTCCTGGGCAATTTCAAAAAGACACTCATTAAACCTTCATAATGAGACCA
GTGCAAGACCTCACTCTTGCCTCTGGAGGCTCACCAAGGAGGGACATCATTGCTTTCAGGAGGAGAATCATTCCTTAGCC
TCCGCTAGGAGGGAGAACATCCAACAGTGCATGAGCCAACCAGAGGTGATGACCTCCCTCTTTGACCTT

Alignment

ORF - retro_ogar_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDLKLERLDFWDSLHGQVPGLLDWDMGNESFLAFTTAHLPLAEQNLARYKLRIVDPPKLPLEKKANADED
          .DLKL....F..SLHGQVPGLLD.DMG.E.FL..TT.H.PLAEQNL..Y.LR...PPK.P.EK....DE.
Retrocopy MDLKLKNCEF*YSLHGQVPGLLD*DMGSELFLPCTTDH*PLAEQNLTKYRLRVMKPPKVPQEKRPSPDEG

Parental  GPEIEPNLWMWVNPNIVFPPGKLEVPESSKREDLASGLPSLQPPKKEEDANGLEATGVELLPLSSSEQCP
          GP..EP.LWMWVNPNIV.P.G..EVP......DL.S..PS.Q.P.K.E..N..EAT.VE.L..SS..Q.P
Retrocopy GPHSEPILWMWVNPNIVCPIGSQEVPKPGXXXDLISMPPSSQLPLKDEESNCSEATVVESLLFSSGKQSP

Parental  PQKQFASPPNNLELTEEEAEDQDDGSSVALPSPHKRAPLQSRRLRQTNSQAGMLWSRPPLNYFHLIALAL
          .QKQF.S.P...ELTEEE.E.QDD.SSVA...P.K.....S..L.Q.N.Q....W..P.LNY.HLIALAL
Retrocopy LQKQFHSSPSDWELTEEETEEQDDSSSVAFQPPNKKKCFKSQKLWQVNNQERRSWPWPLLNYSHLIALAL

Parental  RNSSPCGLNVQQIYSFTRQHFPFFRTAPEGWKNTIRHNLCFRDSFEKV-PVNLQGGAKTRPRSCLWKLTE
          .NS.PCGLNVQ.IY.FT.QHFPFF.TAP.GWKNTI.HNLCF...F.K....NL......RP.SCLW.LT.
Retrocopy KNSHPCGLNVQEIYNFTQQHFPFFWTAPDGWKNTIYHNLCFLGNFKKT>SLNLHNETSARPHSCLWRLTK

Parental  EGHRRFEEEARALASTRLESIQQCMSQPDVMPFLFDL
          EGH..F.EE...LAS.R.E.IQQCMSQP.VM..LFDL
Retrocopy EGHHCFQEENHSLASARRENIQQCMSQPEVMTSLFDL

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_296 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296 ,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,