RetrogeneDB ID: retro_ogar_2642

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873643.1:681745..683584(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028024
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ogar_2642
ATCGTGATCAGGAGCATTTTTTTGTTTCTGGATAGAACCTACATTCTTCAGAATTCAATGCTACCCTCCATTTGGGACAT
GGGCCTGGAGTTATTTAGGGCTCATATCATAAATGATCAGGAAGTTCAGAATAAGACAATTGATGGCATTCTTCTCTTGA
TTGAGAGGGAAAGGAATGGTGAAGCCATTGATAGAAAGTTACTCCAAAGCCTTTTAAGCATGCTCTCTGATCTGCAAATT
TATCAAGATTCTTTTGAACAACGATTTTTGGAAGAAACTAACCGGCTGTATGCAGATGAAGGCCAAAAATTAATGCAAGA
AAGACAGGTTCCCGAATATCTTCATCATGTTAACAAACGCCTAGAAGAAGAAGCAGACAGACTTAATACTTACTTAGCTC
AGACCACCCGGAAGTCATTAATTGCTACTGTAGAAAAACAACTTCTAGGTGAACACTTAACAGCAATTCTTCAGAAAGGT
TTAAATAAGCTCCTGGATGAAAACCGAATTCAAGATTTGTCTCTTCTGTATCAGCTCTTCAGTAGAGTTCAGGGGGGAGT
TCAGGTTCTCTTGCAACAGTGGGTTGACTATATCAAGACATTTGGTGCCACTATTGTAATTAATCCTGAAAAAGATAAAA
CTATGGTTCAAGAACTGCTGGATTTCAAAGACAAAGTTGACCACATAATTGATATCTGCTTTCTGAAGAATGAAAAATTT
ATCAACGCCATGAAGGAAGCATTTGAAACGTTCATTAACAGAAGGCCAAATAAACCTGCGGAACTTATAGCTAAGTATGT
AGATTCAAAGCTTCGTGCGGACAACAAAGGCACTACGGATGAAGAACTTGAGAAAATGTTGGATAAAATTATGATCATAT
TTAGATTCATCCATGGCAAGGATGTTTTTGAGGCCTTCTATAAGAAAGCTTTAGCCAAATGCTTATTAGTTGGGAAGAGT
GCCTCTGTAGATGCCGAAAAGTCAATGCTGTCCAAACTCAAACATGAATGCGGAGCTGCTTTCACCAGCAAACTTGAAGG
AATGTTTAAAGACATGGAACTTTCTAAAGACATCATGATTCAGTTCAAACAGTATATGCAGAGTCAGGATGTACCTGGGA
ATATCGAATTAACTGTGAATATCCTGACAATGGGTTATTGGCCAACGTATGTGCCTATGGAAGTCCATTTACCACCCGAG
ATGGTAAAACTTCAGGAGATTTTCAAGACGTTTTATTTAGGCAAGCACAGTGGCAGGAAACTTCAGTGGCAATCAACCCT
AGGCCACTGTGTGCTAAAAGCAGAATTTAAAGAGGGTAAAAAAGAACTGCAGGTCTCTCTTTTTCAAACACGGGTGCTGC
TAATGTTTAATGAGGGAGAAGAGTTCAGTTTAGAAGAGATCAAGCAGACTACCGGCATAGAGGATGGAGAGTTAAGGAGA
ACGCTGCAATCCTTAGCCTGTGGCAAAGCTAGAGTTCTGGAGAAAAATCCAAAGGGCAAAGATATTGAAGATGGTGACAA
GTTCATTTGTAATGATGATTTCAAACACAGACTTTTCAGGGTAAAGATCAATCAAATACAAATGAAAGAAACAATTGAGG
AACAAGCAAGCACTACGGAAAGGGTATTTCAAGACAGACAGTATCAAATTGACGCTGCGATTGTACGAATTATGAAGATG
AGAAAGACACTTAGCTACAATCTCCTTGTTTCAGAGGTGTACGAGCAATTGAAATTCCCAGTGAAGCCTGCTGATGTTAA
GAAGAGGATAGAATCCTTAATTGACCAGGACTACATGGAAAGAGAGAAAGAAAATCCCAATCAGTACAACTATATTGCA

Alignment

ORF - retro_ogar_2642 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.8 %
• Parental protein coverage: 68.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IMIRSIFLFLDRTYVLQNSMLPSIWDMGLELFRAHIISDQKVQNKTIDGILLLIERERNGEAIDRSLLRS
          I.IRSIFLFLDRTY.LQNSMLPSIWDMGLELFRAHII.DQ.VQNKTIDGILLLIERERNGEAIDR.LL.S
Retrocopy IVIRSIFLFLDRTYILQNSMLPSIWDMGLELFRAHIINDQEVQNKTIDGILLLIERERNGEAIDRKLLQS

Parental  LLSMLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLDEEADRLITYLDQTTQKSL
          LLSMLSDLQIYQDSFEQRFLEETNRLYA.EGQKLMQER.VPEYLHHVNKRL.EEADRL.TYL.QTT.KSL
Retrocopy LLSMLSDLQIYQDSFEQRFLEETNRLYADEGQKLMQERQVPEYLHHVNKRLEEEADRLNTYLAQTTRKSL

Parental  IATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYIKAFGSTIVINPE
          IATVEKQLLGEHLTAILQKGLN.LLDENRIQDLSLLYQLFSRV.GGVQVLLQQW..YIK.FG.TIVINPE
Retrocopy IATVEKQLLGEHLTAILQKGLNKLLDENRIQDLSLLYQLFSRVQGGVQVLLQQWVDYIKTFGATIVINPE

Parental  KDKTMVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFINKRPNKPAELIAKYVDSKLRAGNKEATD
          KDKTMVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFIN.RPNKPAELIAKYVDSKLRA.NK..TD
Retrocopy KDKTMVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFINRRPNKPAELIAKYVDSKLRADNKGTTD

Parental  EELEKMLDKIMIIFRFIYGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFK
          EELEKMLDKIMIIFRFI.GKDVFEAFYKK.LAK.LLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFK
Retrocopy EELEKMLDKIMIIFRFIHGKDVFEAFYKKALAKCLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFK

Parental  DMELSKDIMIQFKQYMQNQNVPGNIELTVNILTMGYWPTYVPMEVHLPPEMVKLQEIFKTFYLGKHSGRK
          DMELSKDIMIQFKQYMQ.Q.VPGNIELTVNILTMGYWPTYVPMEVHLPPEMVKLQEIFKTFYLGKHSGRK
Retrocopy DMELSKDIMIQFKQYMQSQDVPGNIELTVNILTMGYWPTYVPMEVHLPPEMVKLQEIFKTFYLGKHSGRK

Parental  LQWQSTLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEEFSLEEIKQATGIEDGELRRTLQSLACGKA
          LQWQSTLGHCVLKAEFKEGKKELQVSLFQT.VLLMFNEGEEFSLEEIKQ.TGIEDGELRRTLQSLACGKA
Retrocopy LQWQSTLGHCVLKAEFKEGKKELQVSLFQTRVLLMFNEGEEFSLEEIKQTTGIEDGELRRTLQSLACGKA

Parental  RVLSKNPKGKDIEDGDKFICNDDFKHKLFRIKINQIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKM
          RVL.KNPKGKDIEDGDKFICNDDFKH.LFR.KINQIQMKET.EEQASTTERVFQDRQYQIDAAIVRIMKM
Retrocopy RVLEKNPKGKDIEDGDKFICNDDFKHRLFRVKINQIQMKETIEEQASTTERVFQDRQYQIDAAIVRIMKM

Parental  RKTLSHNLLVSEVYNQLKFPVKPADLKKRIESLIDRDYMERDKENPNQYNYIA
          RKTLS.NLLVSEVY.QLKFPVKPAD.KKRIESLID.DYMER.KENPNQYNYIA
Retrocopy RKTLSYNLLVSEVYEQLKFPVKPADVKKRIESLIDQDYMEREKENPNQYNYIA

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_2642 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,