RetrogeneDB ID: retro_ogar_3297

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873770.1:211384..212655(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025569
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBBP4
• Ensembl ID: ENSOGAG00000011632
• Aliases: None
• Description: retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]

Sequence

>retro_ogar_3297
ATGGCGAGTAAAGAGATGTTTGAAGATACTGTGGAGGAGCGTGTCATCAATGAAGAATATAAAATCTGGAAGAATACACC
ATTTCTGTATGACCCGGTTATGACCCATGCTCTTCAGTGGCCCAGTCTTACCGTTCAGTGGCTTCCTGAAGTGACTAAAC
CTGAAGAGAAGGATTAGGCCCTTCATTGGTGCTGGGGACTCATACGTCTGATGAGCAGACTCATCCGTTGGTTGCTCAAG
TACATATTCCCAATGATGATGCACAGTTTGATGCTTCCCATTGTGACAGTGACAGGGGTGAATTTGGTGGCTTTGGCTCT
ATAACAGGAAAAATTGAATGTGAAATTAAAATTAATCATGAAGGAGAAGTAAACCGTGCTCGGTACATGCCGCAGAATCC
TCACATCATTGCTACAAAAACACCATCTTCTGCTGTGTTGGGTTTTGACTATACAAAACATCCCGCTAAACCAGACCCAA
GTGGAGAATGTAATCCTGATCTTGGGTTAAGAGGTCACCAGAAGGAAGGCTATGGTCTTTCCTGGGATTCTAATTTGAGT
GGACATCTCCTAAGTGCATCTGACGACCATACGGTCTGTCTGTGGGATATAAATGCAGGACCAAAGGAAGGCAAAATTGT
GGATGCCAAGGCGATCTTTACTGGCCACTCAGCTGTTGTGGAGGATGTGGCCTGGCATCTGCTGCACAAGTCATTGTTTG
GATCTGTTGCTGATGATCAGAAACTTATGATGTGGGACACCAGGTCCAATACCACCTCCAAACCAAGCCATTTGGTGGAT
GCCCACACTGCTGAGGTCAACTGCCTCTCATTCAATCCCTCCAGCGAGTTCATTCTAGCAACCGGCTCTGCGGATAAGAC
CGTAGCTTTATGGGATCTGCGTAACTTAAAATTAAAACTCCATACCTTTGAATCACATAAAGACGAAATTTTTCAGGTCC
ACTGGTCTCCACATAAGGAAACTATTCTGGCTTCCAGTGGTACTGATCGCCGCCTGAATGTGTGGGATTTAAGTAAAATT
GGAGAAGAACAGTCAGCAGAAGATGCAAAAGATGGGCCTCCTGAACTCCTGTTCATTCATGGAGGACACACTGCCAAGAT
TTCAGATTTTTTTAGTTGGAACCCCAATGAGCCTTGGGTCATTTGCTCAGTGTCTGAGGATAACATCATGCAGATATGGC
AAATGGCTGAAAATATTTACAATGATGAAGAGTCAGATGTCACACCATCGGAACTGGAGGGACAAGGATCT

Alignment

ORF - retro_ogar_3297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTSRP-RPGSNPPALVYV
          MA.KE..F.D.VEERVINEEYKIW.KNTPFLYD.VMTHAL.WPSLT.QWLP.VT....R.G..P......
Retrocopy MASKEM-FEDTVEERVINEEYKIW-KNTPFLYDPVMTHALQWPSLTVQWLPEVTKPE<REGLGPSLVL--

Parental  AGTLLTELQNYVMVFSLKNPPPHTYHSGTHEDSQQREFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNP
          .GT.....Q....V.....P.........H.DS...EFGGFGS..GKIE.EIKINHEGEVNRARYMPQNP
Retrocopy -GTHTSDEQTHPLVAQVHIPNDDAQFDASHCDSDRGEFGGFGSITGKIECEIKINHEGEVNRARYMPQNP

Parental  CIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDI
          .IIATKTPSS.VL.FDYTKHP.KPDPSGECNPDL.LRGHQKEGYGLSW..NLSGHLLSASDDHT.CLWDI
Retrocopy HIIATKTPSSAVLGFDYTKHPAKPDPSGECNPDLGLRGHQKEGYGLSWDSNLSGHLLSASDDHTVCLWDI

Parental  SAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVN
          .A.PKEGK.VDAK.IFTGH.AVVEDV.WHLLH.SLFGSVADDQKLM.WDTRSN.TSKPSH.VDAHTAEVN
Retrocopy NAGPKEGKIVDAKAIFTGHSAVVEDVAWHLLHKSLFGSVADDQKLMMWDTRSNTTSKPSHLVDAHTAEVN

Parental  CLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDL
          CLSFNP.SEFILATGSADKTVALWDLRNLKLKLH.FESHKDEIFQV.WSPH.ETILASSGTDRRLNVWDL
Retrocopy CLSFNPSSEFILATGSADKTVALWDLRNLKLKLHTFESHKDEIFQVHWSPHKETILASSGTDRRLNVWDL

Parental  SKIGEEQSPEDAEDGPPELLFIHGGHTAKISD-FSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEG
          SKIGEEQS.EDA.DGPPELLFIHGGHTAKISD.FSWNPNEPWVICSVSEDNIMQ.WQMAENIYNDE....
Retrocopy SKIGEEQSAEDAKDGPPELLFIHGGHTAKISDFFSWNPNEPWVICSVSEDNIMQIWQMAENIYNDEESDV

Parental  S-VDPEGQGS
          .....EGQGS
Retrocopy TPSELEGQGS

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_3297 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 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001021	7 retrocopies	retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus	ENSCPOG00000015352	3 retrocopies	retro_cpor_154, retro_cpor_27, retro_cpor_899,
Gorilla gorilla	ENSGGOG00000011313	4 retrocopies	retro_ggor_1022, retro_ggor_1314, retro_ggor_1867, retro_ggor_2428,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Mustela putorius furo	ENSMPUG00000015214	1 retrocopy	retro_mputfur_104,
Otolemur garnettii	ENSOGAG00000011632	2 retrocopies	retro_ogar_3079, retro_ogar_3297 ,
Otolemur garnettii	ENSOGAG00000014995	1 retrocopy	retro_ogar_2220,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sarcophilus harrisii	ENSSHAG00000010923	1 retrocopy	retro_shar_399,
Tupaia belangeri	ENSTBEG00000002236	3 retrocopies	retro_tbel_1360, retro_tbel_1718, retro_tbel_3802,
Vicugna pacos	ENSVPAG00000011876	4 retrocopies	retro_vpac_333, retro_vpac_419, retro_vpac_652, retro_vpac_94,