RetrogeneDB ID: retro_ogar_3309

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873773.1:66563..67670(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ogar_3309
AAGGATCCAGATGAAGAAATTGCCAAAATTGACAGGACTGTGAGAGGCCAGTGTGGCAGCAGTCAGGCTTGGGACAGTAA
CAGTCTGTGCAAACCCCTGTTCCTTGATCCCCACACCTGACAAAGAGGAGGATGAGCTGGTGTGCCCGACTCCAACGTAC
AAGCCTCAGGTCACTCTGTCCAGGGCCTCCACACTGCCTATGCTGAACTGGGCAAATTGAGAGGAAGTCTGGAAGATCAT
GCCGCACAAGGAGAAGATGTACCTGTGGGACCAGCACCTGCTGCAGCGGCATCCTCTGCTGCAGCCTCACATGCGCGCCA
TCAACCTGGACTGGCTGATGGAGGTGTGTGAAGTCTACAAACTCCACAGGGAGACGTTCTACTTGGCACAGGATTTCTTT
GATCAGTATATGGCAACACAAGAGAACGTTGTGAAAACACTTCTACAGTTTATTGGGATTTCATCATTATTTATTGCAGC
CAAACTTGAGGAAATCTATCCTCCAAAGTTGCACCAGTTTGCTTATGTCACTGATGTGGCTTGTTCAGGAGATGAAATTC
TTACCATGGAATTAATGATTATGAAGGCTCTTAAGTGGCACTAAGTCCCCTGACCATTGTGTCCTGGCTGAATGTGTACC
TGCAGGTCACAAATCTGAATGACTTATATGAAGTGCTCTTGCAACAGTATCCTCAGCAGATCTTTATTCAGATTGCAGAG
CTCTTAGACCTCTGCATCCTGGATGTGGACTACTTAGAATTTTTCTAAGGGGTGCTCAGTGCTTCTGCCTTGTATCATTT
CTCTTTGTCTGAAGTGATGCAAAAGGTTTCAGGGTATCAGTGATGTGACACAGAGCACTGTGTCAAGTGGACGGTCCCAT
TTGCCTTGGTCATCAGGGAGACAGGCAGCTCGAAGCTGAAGCACTTCAGGGGGGTTCCTACGGATGATGCACACAACATC
CAGACCCATAGGGACAGCTTGGACTTGCTGGACAAAGCCCAAGCAAAGAAAGCCATACTGTCTGAACAGAATAGGATTTC
TCCTGTGCCCACTGGTGTCCTCACCCTGCCACACAGCAATAAGAAGCAGAGTGATGAGCAGGGGACA

Alignment

ORF - retro_ogar_3309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.9 %
• Parental protein coverage: 90.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QDPDEEIAKIDKTVRGQCGSSQSWDSNTVCANPCSL-IPTPDKEEDELVYPTPTYKPQITPSRASPLPLL
          .DPDEEIAKID.TVRGQCGSSQ.WDSN..C..P..L.IPTPDKEEDELV.PTPTYKPQ.T.SRAS.LP.L
Retrocopy KDPDEEIAKIDRTVRGQCGSSQAWDSNSLC-KPLFL>IPTPDKEEDELVCPTPTYKPQVTLSRASTLPML

Parental  NWANREEVWKIMLNKEKTYLRDQHLLQRHPLLQPHMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMA
          NWAN.EEVWKIM..KEK.YL.DQHLLQRHPLLQPHMRAI.LDWLMEVCEVYKLHRETFYLAQDFFD.YMA
Retrocopy NWAN*EEVWKIMPHKEKMYLWDQHLLQRHPLLQPHMRAINLDWLMEVCEVYKLHRETFYLAQDFFDQYMA

Parental  TQENIVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWR-LSPLTIV
          TQEN.VKTLLQ.IGISSLFIAAKLEEIYPPKLHQFAYVTD.ACSGDEILTMELMIMKALKW..LSPLTIV
Retrocopy TQENVVKTLLQFIGISSLFIAAKLEEIYPPKLHQFAYVTDVACSGDEILTMELMIMKALKWH<LSPLTIV

Parental  SWLNVYLQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEFSYGVLAASALYHFSSSELMQKVS
          SWLNVYLQV..LNDL.EVLL.QYPQQIFIQIAELLDLC.LDVD.LEF..GVL.ASALYHFS.SE.MQKVS
Retrocopy SWLNVYLQVTNLNDLYEVLLQQYPQQIFIQIAELLDLCILDVDYLEFF*GVLSASALYHFSLSEVMQKVS

Parental  GYQWCDIEHCVKWMVPFAMVIRETGSSKLKHFRGVPADDAHNIQTHRDSLDLLDKAQAKKAILSEQNRIS
          GYQ.CD.EHCVKW.VPFA.VIRETGSSKLKHFRGVP.DDAHNIQTHRDSLDLLDKAQAKKAILSEQNRIS
Retrocopy GYQ*CDTEHCVKWTVPFALVIRETGSSKLKHFRGVPTDDAHNIQTHRDSLDLLDKAQAKKAILSEQNRIS

Parental  PVPTGVLTPPHSSKKQSDEQGT
          PVPTGVLT.PHS.KKQSDEQGT
Retrocopy PVPTGVLTLPHSNKKQSDEQGT

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_3309 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,