RetrogeneDB ID: retro_ogar_3040

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873701.1:5030..5978(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSOGAG00000014216
• Aliases: None
• Description: RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]

Sequence

>retro_ogar_3040
GTGACAAATGTGCAGCCCAAAGCAGTATCAACACCAGCACACTCTGCAGCTCAGCAATCAAATCCTGTCACCACCACCTC
CACAGCAACAACTGCGGCTCAGGCCCCAGCCCTTGCCCGGCTCCCGCATCCGTTACTCCAGCATCAACAACATCTGCCGA
ACCTGCACCGCTAGTGCAGCTAAACAAAAGCAACCTGCAGAAAAGCCAGCACAGACACCAACTGATAGTACACCAGCGGG
TTCCTCCCGGTGAAACTTGTTGAAGATGCACGTGCCCTTGTGACAGGTCAGTCTTATGAGATATGGTAACTGAGATCATG
TCAATGGGCTATGAACGAGAGCAAGTAATCACAGCCCTGAGAGCCAGTTTCAACAACCCTGGCAGAGCAGTGGACTATCT
TTTAATGGGAATCCCTGGAGATAGAGAAAATCAGGCTGTGGTTGACCCCCCTCAGGCGGCTGGCACTGGGACTCCTCAGT
CTTCAGCAACGGCGGCGGTGGCAGCAACTACCACAGCGACAACTACGACAAGTTCTGGAGGACATCCCCTTGAAGTTTTG
GGGAATCAGCCTCGATTTCAACAAATGAGACAAATTATTCAACAAAATCCTTCCCTGCTTCCAGCATTGCTACAACATAG
ACAGAGAGAATCCTCAGTTACTGCAACAAATTAGCCAACACCCGGAGCATTTTATTCAGACGTTAAATGAACCAGTTGGA
GAAGCTGGTGGTCAGGGAGGAGGAGGAGGAGGTGGCAGTGGAGGAATTGCTGAAGCTGGAAGCAGTCACCTGAACTACAG
TCAAGTTAGGTCTCAGGAGAAAGAAGCTGTGGAAAGGTTAAAGGCATTAGGATTTCTTGAAGGACTTGTGATACAAGCAT
AGTTTGCTTGTGAGAAGAATGAGAATTTGGCTGCCAATTTTCTTCTACAGCAGAACTTTGATGAAGAT

Alignment

ORF - retro_ogar_3040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.21 %
• Parental protein coverage: 80.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VSTPAPAAAAAQQSNPVTTTPVTSSTATTVAQAPTPA-PAPASTPVSVTPASTTTSPEPAP-ASATKQEK
          V....P.A.................T.T....A..PA.P.PA..P.SVTPASTT.S.EPAP.ASA.KQ..
Retrocopy VTNVQPKAVSTPAHSAAQQSNPVTTTSTATTAAQAPA<PCPA--PASVTPASTT-SAEPAP<ASAAKQKQ

Parental  PAEKPAETPVATSPTPTDSTSGDSSRSNLF-EDATSALVTGQSYE-NMVTEIMSMGYEREQVIAALRASF
          ....PAE.P.....TPTDST...SSR.NL..EDA..ALVTGQSYE..MVTEIMSMGYEREQVI.ALRASF
Retrocopy ----PAEKP---AQTPTDSTPAGSSR*NLL<EDAR-ALVTGQSYE<DMVTEIMSMGYEREQVITALRASF

Parental  NNPDRAVEYLLMGIPGDRESQAVVDPPQAAGTGTPQSSAVAAAAATTTATTTTTTSSGGHPLEFLRNQPQ
          NNP.RAV.YLLMGIPGDRE.QAVVDPPQAAGTGTPQSSA.AA.AATTTATTTT..SSGGHPLE.L.NQP.
Retrocopy NNPGRAVDYLLMGIPGDRENQAVVDPPQAAGTGTPQSSATAAVAATTTATTTT--SSGGHPLEVLGNQPR

Parental  FQQMRQIIQQNPSLLPALLQQ-IGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGGGGSGGIA
          F.Q....I.Q....L...L.Q.I.RENPQLLQQISQH.EHFIQ.LNEPV.EAGGQ...GGGGGGGSGGIA
Retrocopy F-QQMRQIIQQNPSLLPALLQ>IDRENPQLLQQISQHPEHFIQTLNEPVGEAGGQ---GGGGGGGSGGIA

Parental  EAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
          EAGS.H.NY.QV..QEKEA.ERLKALGF.EGLVIQA.FACEKNENLAANFLLQQNFDED
Retrocopy EAGSSHLNYSQVRSQEKEAVERLKALGFLEGLVIQA*FACEKNENLAANFLLQQNFDED

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_3040 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040 ,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,