RetrogeneDB ID: retro_ogar_977

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873532.1:28061432..28061888(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCND2
• Ensembl ID: ENSOGAG00000005208
• Aliases: None
• Description: cyclin D2 [Source:HGNC Symbol;Acc:1583]

Sequence

>retro_ogar_977
GAGTGGGAGCTGGTAGTCCTGGGGAAGTTGAAGTGGAACCTGGCTGCTGTCACTCCTCATGACTTCATTGAGCACATCCT
TCGCAAGTTGTCGCAGCTGAGGGAGAAGCTGTCTCTGATCCACAAGCACACACAGACCTTCAACGCTCTGTGTGCCACTG
ACTTTAAGTTGGCCATGTACCTACCGTTGATGACGGCAACTGGAATTGTGGATACAGCCACCTGCAGGCTTCAGCAGGAT
GAGGAAGTGAGCTAGCTCACTTGCGATGCCCTGACCGAGCTGCTGGCCAAGATCACCAACACAGATGTGGATTGTCTCAA
AGCCTGCCAGGAGCAGATCGAGGCAGTGCTTCTCAATAGCCTGCAGCAGTACTGTCAGGACCAGCACGATGGATCTAAGT
CAGAGGATGAACTGGACCAAGCCAGCACCCCTACAGATGTGCGGGATATTGACCTG

Alignment

ORF - retro_ogar_977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.82 %
• Parental protein coverage: 52.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EWELVVLGKLKWNLAAVTPHDFIEHILRKLPQQREKLSLIRKHAQTFIALCATDFKFAMYPPSMIATGSV
          EWELVVLGKLKWNLAAVTPHDFIEHILRKL.Q.REKLSLI.KH.QTF.ALCATDFK.AMY.P.M.ATG.V
Retrocopy EWELVVLGKLKWNLAAVTPHDFIEHILRKLSQLREKLSLIHKHTQTFNALCATDFKLAMYLPLMTATGIV

Parental  GAAICGLQQDEEVSSLTCDALTELLAKITNTDVDCLKACQEQIEAVLLNSLQQYRQDQRDGSKSEDELDQ
          ..A.C.LQQDEEVS.LTCDALTELLAKITNTDVDCLKACQEQIEAVLLNSLQQY.QDQ.DGSKSEDELDQ
Retrocopy DTATCRLQQDEEVS*LTCDALTELLAKITNTDVDCLKACQEQIEAVLLNSLQQYCQDQHDGSKSEDELDQ

Parental  ASTPTDVRDIDL
          ASTPTDVRDIDL
Retrocopy ASTPTDVRDIDL

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_977 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001593	1 retrocopy	retro_cjac_3884,
Felis catus	ENSFCAG00000000138	1 retrocopy	retro_fcat_809,
Oryctolagus cuniculus	ENSOCUG00000015589	1 retrocopy	retro_ocun_1277,
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,