RetrogeneDB ID: retro_ogar_930

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:24726203..24727423(-)
• Located in intron of: ENSOGAG00000012095

Retrocopy information

• Ensembl ID: ENSOGAG00000027308
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNE1
• Ensembl ID: ENSOGAG00000006217
• Aliases: None
• Description: cyclin E1 [Source:HGNC Symbol;Acc:1589]

Sequence

>retro_ogar_930
ATGCCAAGGGAGAGGAGAGAGAAGGGTGCGAAAGAACGGGGTGCTGTGAAGGAGAAAGGTAGAGTGGATTTCTCTGTTCG
CTCCAGGAAAAGGAAGGCAAATGTGGCCACTTTTTTTGCAGGATCCAGAGGAAGAAATTGCCAAAATTGACAGGACTGTG
AGAGGCCAGTGTGGCAGCAGTCAATCTTGGGACAGTAACACAGTCTGTGCAAACCCCTGTTCCTTGATCCCCACACCTGA
CAAAAAGGATGAGCTGGTATACCCGACTCCGATGTACAAGCCTCAGATCACGCCATCCAGGGTCTCCCTATTGCCTATGC
TAAACTGGGCAAATCAAGAGGAAGTCTGGAAGATCATGCTGAACAAGGAGAAGACGTACCTGTGGGACCAGCACCTGCTG
CAGCGGTACCCTCTGCTGCAGCCTCACATGTGCGCCATCCTCCTGGACTGGCTGATGGAGGTGTGTGAAGTCTATAAACT
TCACAGGGAGACGTTCTACTTGGCACAGGATTTCTTTGATCAGTATATGGCAACACAAGAGAACGTTGTGAAAACACTTC
TACAGCTTATTGGGATCTCATCTTTATTGTAGCCAAACTTGAGGAAAGCTATTCTCCAAAGTTGCACCAGTTTGCTTATG
TTACAGATGGGGCTTATTCAGGAGATGAAATTCTTACCATAGAATTAATGATTATGAAGGCTCGTAAGTGGCATTTAAAT
CCCCTGACCATTGTGTCCTGGCTGAATGTGTACTTACAGGTCACATATCTGAACGACTTATATGAAGTGCTCTTGCCACA
GTATCCTCAGCAGATCTTTATTCAGATTGCAGAGCTCTTAGATCTCTGCATCCTGGATGCGGACTGCTTAGAATTTTCCT
ACGGGTGCTCACTGCTTCTGCCTTGTATCATTTCTCTTCATCTGAACTGATGCAAAAGGTTTCAGGGTATCAGTGGTGTG
ACATAGAGCACTGTATCAAGTGGATGGTCCCATTTGCCATGGTCATCAGGGAGACAGGGAGCTCGAAGCTGAAGCACTTT
AGGGGGGTTGCTGCAGATGATGCACACAACATCCAGACCCATAGGGACAGCTTGGACTTGCTGGACAAAGCCCAAGCAAA
GAAAGCCATACTGTCTGAACAGTATAAGATTTCTCCTGTGCCCACTGGGATCCTCACCCCACCACACAGCAGTAAGAAGC
AGAGTGATGAGCAGGGGACG

Alignment

ORF - retro_ogar_930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPRERRERDAKERGSVKEEGGMDFSVRSRKRKANVA-VFLQDPDEEIAKIDKTVRGQCGSSQSWDSNTVC
          MPRERRE..AKERG.VKE.G..DFSVRSRKRKANVA..FLQDP.EEIAKID.TVRGQCGSSQSWDSNTVC
Retrocopy MPRERREKGAKERGAVKEKGRVDFSVRSRKRKANVA>LFLQDPEEEIAKIDRTVRGQCGSSQSWDSNTVC

Parental  ANPCSLIPTPDKEEDELVYPTPTYKPQITPSRASPLPLLNWANREEVWKIMLNKEKTYLRDQHLLQRHPL
          ANPCSLIPTPDK..DELVYPTP.YKPQITPSR.S.LP.LNWAN.EEVWKIMLNKEKTYL.DQHLLQR.PL
Retrocopy ANPCSLIPTPDKK-DELVYPTPMYKPQITPSRVSLLPMLNWANQEEVWKIMLNKEKTYLWDQHLLQRYPL

Parental  LQPHMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENIVKTLLQLIGISSL-FIAAKLEEIYPP
          LQPHM.AILLDWLMEVCEVYKLHRETFYLAQDFFD.YMATQEN.VKTLLQLIGISSL...A...E...P.
Retrocopy LQPHMCAILLDWLMEVCEVYKLHRETFYLAQDFFDQYMATQENVVKTLLQLIGISSL<IVAKLEESYSP-

Parental  KLHQFAYVTDGACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYLQVAYLNDLHEVLLPQYPQQIFIQI
          KLHQFAYVTDGA.SGDEILT.ELMIMKA.KW.L.PLTIVSWLNVYLQV.YLNDL.EVLLPQYPQQIFIQI
Retrocopy KLHQFAYVTDGAYSGDEILTIELMIMKARKWHLNPLTIVSWLNVYLQVTYLNDLYEVLLPQYPQQIFIQI

Parental  AELLDLCVLDVDCLEFSYG-VLAASALYHFSSSELMQKVSGYQWCDIEHCVKWMVPFAMVIRETGSSKLK
          AELLDLC.LD.DCLEFSYG.VL.ASALYHFSSSELMQKVSGYQWCDIEHC.KWMVPFAMVIRETGSSKLK
Retrocopy AELLDLCILDADCLEFSYG<VLTASALYHFSSSELMQKVSGYQWCDIEHCIKWMVPFAMVIRETGSSKLK

Parental  HFRGVPADDAHNIQTHRDSLDLLDKAQAKKAILSEQNRISPVPTGVLTPPHSSKKQSDEQGT
          HFRGV.ADDAHNIQTHRDSLDLLDKAQAKKAILSEQ..ISPVPTG.LTPPHSSKKQSDEQGT
Retrocopy HFRGVAADDAHNIQTHRDSLDLLDKAQAKKAILSEQYKISPVPTGILTPPHSSKKQSDEQGT

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_930 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676,
Otolemur garnettii	ENSOGAG00000005208	1 retrocopy	retro_ogar_977,
Otolemur garnettii	ENSOGAG00000006217	2 retrocopies	retro_ogar_3309, retro_ogar_930 ,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770, retro_ogar_2766,
Otolemur garnettii	ENSOGAG00000034667	1 retrocopy	retro_ogar_1793,
Sus scrofa	ENSSSCG00000002855	1 retrocopy	retro_sscr_232,
Vicugna pacos	ENSVPAG00000001390	1 retrocopy	retro_vpac_219,