RetrogeneDB ID: retro_ogar_2069

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873587.1:1455929..1457387(-)
• Located in intron of: ENSOGAG00000001067

Retrocopy information

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

Parental gene information

• Parental gene symbol: CUL4B
• Ensembl ID: ENSOGAG00000001282
• Aliases: None
• Description: cullin 4B [Source:HGNC Symbol;Acc:2555]

Sequence

>retro_ogar_2069
TGCAGACAACTAATTATGATGAGGAGCTTTTTTTTTGTTTCTGGACAGAACTTATGTTCTTCAGAATTCAATGCTACCCT
CTATTTGGGACATGGGTCCGGAGGCCCATAGCATAAATGATCAGAAAGTTCAGAATAAGACAATTGATGGCATTCTTCTC
TTGATTAAGAGGGAAAGGAATGGTGCAGCAATTGATAGAAGTTTACTCTGAAGCCTTTTAAGCATGCTCTCTGGTTTGCA
AATTTATCAAGATTCTTTTGAAAAACGATTTTTGGAAGAAACTAACTGGCTGTATGCAGCTGAAGGCCAAAAATTAATGC
AAGAAAGAGAGGTTCCTGAATATCTTCATTATTTTAACAAATGTCTAGAAGAAGAAGCAGACAGACTTATTACTTACTTA
GATCAGACCACCCAGAAGTCATTAATTACTACTGTAGAAAAACAACTGCTTGGTGAACACATAACAGCAATTCTTTAGAA
AGGTTTAAATAACCTCTTTGATGAACACTGAATTCAAGATTTGTCTCTTCTGTATCAGCCCTTCAGTAGAGTTTGAGGTG
GAGTTCAGGTTCTCTAGCAACAGTGGATTGAATATATTAAGGCATTTGGTAACAGTATTGTAATTAATCCTGAAAAAGAT
AAAACTATGGTTCAAGAACTACTGGATTTTAAAGATAAAGTTGACCACATAATTGATATCTGCTTTCTGAAGAATGAAAA
ATTTATCAATACCATGAAAGAAGCATTTGAAACATTCATTAACAAAAGACCAAATAAACGTGCTGAACTTATAACTTAAG
TATATAGATTCAAAGCTTCATGTAGCCAACAAAGAAGCTACAGATGAAGAACTTGAGAAAATGTTGGATAAAATTATGAT
CATATTTAGATTTATATATGGCAAGGGTGTTTTTGAGGGCTTTTATAAGAAAGATTTAGCCAAATGCTTATTAGTTGGGA
AGAGTGCATCTGTAGATGCTGAAAAGTCAATGCTGTCCAAACTCAAACATGAATGTGGAGCTGTTTTCACCAGCAAACTT
GAAGGAATGTTTAAAGACATGGAACTCTCTAAAGACATTATGATTCAGTTCAAACAGTATATACAGAGTCAGAATGTACC
TGGAGATATTGAATTAACTGTGAATATCCTGACAATGGGTTATTGGCCAACATACGTGCGTATGGAACTCCCTTTACCAC
CAGAGATGGTAAAACTTCAGGAAATTTTCAAGACGTTTTATTTAGGCAAGCACAGCGGTAGGAAACTTCAGTGGCAATTA
GCCCTAGGACACTATGTGCTAAAAGCAGAATTTAAAGAGGGTAAAAAAAGGACTCCAGGTCTTTCTTCTTCAAACACTGG
TGCTGCTAATGTTTAATGAGGGAGAAGAGTTCAGTTTAGAAGAGATCAAGCAGGCTACCAGAATAGAGGATGGAGAGTTA
AGAAGAACACTCTACAGT

Alignment

ORF - retro_ogar_2069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.37 %
• Parental protein coverage: 54.89 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CFVTIMIRSIFL-FLDRTYVLQNSMLPSIWDMGLELFRAHIISDQKVQNKTIDGILLLIERERNGEAIDR
          C...IM.RS....FLDRTYVLQNSMLPSIWDMG.E...AH.I.DQKVQNKTIDGILLLI.RERNG.AIDR
Retrocopy CRQLIMMRSXXX>FLDRTYVLQNSMLPSIWDMGPE---AHSINDQKVQNKTIDGILLLIKRERNGAAIDR

Parental  SLLRSLLSMLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLDEEADRLITYLDQT
          SLL.SLLSMLS.LQIYQDSFE.RFLEETN.LYAAEGQKLMQEREVPEYLH..NK.L.EEADRLITYLDQT
Retrocopy SLL*SLLSMLSGLQIYQDSFEKRFLEETNWLYAAEGQKLMQEREVPEYLHYFNKCLEEEADRLITYLDQT

Parental  TQKSLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYIKAFGSTI
          TQKSLI.TVEKQLLGEH.TAIL.KGLNNL.DE..IQDLSLLYQ.FSRV.GGVQVL.QQWIEYIKAFG..I
Retrocopy TQKSLITTVEKQLLGEHITAIL*KGLNNLFDEH*IQDLSLLYQPFSRV*GGVQVL*QQWIEYIKAFGNSI

Parental  VINPEKDKTMVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFINKRPNKPAELIA-KYVDSKLRAG
          VINPEKDKTMVQELLDFKDKVDHIIDICFLKNEKFIN.MKEAFETFINKRPNK.AELI..KY.DSKL...
Retrocopy VINPEKDKTMVQELLDFKDKVDHIIDICFLKNEKFINTMKEAFETFINKRPNKRAELIT>KYIDSKLHVA

Parental  NKEATDEELEKMLDKIMIIFRFIYGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSK
          NKEATDEELEKMLDKIMIIFRFIYGK.VFE.FYKKDLAK.LLVGKSASVDAEKSMLSKLKHECGA.FTSK
Retrocopy NKEATDEELEKMLDKIMIIFRFIYGKGVFEGFYKKDLAKCLLVGKSASVDAEKSMLSKLKHECGAVFTSK

Parental  LEGMFKDMELSKDIMIQFKQYMQNQNVPGNIELTVNILTMGYWPTYVPMEVHLPPEMVKLQEIFKTFYLG
          LEGMFKDMELSKDIMIQFKQY.Q.QNVPG.IELTVNILTMGYWPTYV.ME..LPPEMVKLQEIFKTFYLG
Retrocopy LEGMFKDMELSKDIMIQFKQYIQSQNVPGDIELTVNILTMGYWPTYVRMELPLPPEMVKLQEIFKTFYLG

Parental  KHSGRKLQWQSTLGHCVLKAEFKEGKKE-LQVSLFQTLVLLMFNEGEEFSLEEIKQATGIEDGELRRTLQ
          KHSGRKLQWQ..LGH.VLKAEFKEGKK..LQV.L.QTLVLLMFNEGEEFSLEEIKQAT.IEDGELRRTL.
Retrocopy KHSGRKLQWQLALGHYVLKAEFKEGKKR>LQVFLLQTLVLLMFNEGEEFSLEEIKQATRIEDGELRRTLY

Parental  S
          S
Retrocopy S

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_2069 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010345	1 retrocopy	retro_mdom_793,
Oryctolagus cuniculus	ENSOCUG00000015633	1 retrocopy	retro_ocun_349,
Otolemur garnettii	ENSOGAG00000001282	2 retrocopies	retro_ogar_2069 , retro_ogar_2642,
Otolemur garnettii	ENSOGAG00000005046	3 retrocopies	retro_ogar_1871, retro_ogar_2954, retro_ogar_804,
Otolemur garnettii	ENSOGAG00000014715	1 retrocopy	retro_ogar_3491,
Sarcophilus harrisii	ENSSHAG00000011426	1 retrocopy	retro_shar_682,