RetrogeneDB ID: retro_ogar_3057

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873705.1:2353172..2354389(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSOGAG00000014848
• Aliases: None
• Description: isocitrate dehydrogenase 1 (NADP+), soluble [Source:HGNC Symbol;Acc:5382]

Sequence

>retro_ogar_3057
AGTGGTAGTTCTGTGGTAGAGATGCAAATGACATGAATCACTTGGGAGTTGATAAAAGAAAAACTCTTTTTTCCTTAAAT
GGAATTGGATCTACATAGCTATGATTTAGGCATAGAGAATTGTGATGCCACCAGCAGCCAAGTCCCCAAGGATGCCGCAG
AAGTCATAAAGAAATATAACACAGGAGTCTAGGGTGCTACTATCACCCCTGATGAGAAAAGGGTTGAGGAACTCAAGATG
AAACAAATGTGGAAATCACCGAATGACACCATCCTAAATATTCTGAGCGGAACTATCTTCAGGGAAGCTATTATCTTCAA
AAACATCCCCTGGCTTGGGAGTTGATGGGTGAAACCCATCATCATAGGTCATCATGCTTATGCGGACCAATACAGAGCAA
CCAATTTTGTTGTTCCTGGGACTGGAAAAGTAGAGATAACATACACACCAAGTGATGGAACCCAAAAGGTGACATACTTG
GTATATAAGTTTGAAGATGGTGGTGGTGTTGCCATGGGTATGTACAATCAAGAAAAATCAGTCAAAGATTTTGCACACTT
CCTTCCAATGGCTCTGTCTAAGGTTTGGCCTTTGTATCTAAGTACCAAAAACAATATTCTGGAGAAATAATATGGACCCT
TAAAGACATCTTTCAGGAGATGTATGACAAGCAGGACAAATCCCAATTTGAAGCCCAGAAGATCTGATAGAGCATAGGCT
CATATCAATGGCATAGTGGCTCAAGCTATGAAATCAGAGGGAAGCTTCATCTGGTCCTGAAAAAACTATGATAGTGATGT
GAATTCGGACTCCATGGCCCAAGGTTATGACTCTCTTGGCATGATGACCAGTGTGCTGGTTTGTCCACATGGCAAGACAG
TAGAAGCAGAGGCAGCCCATGGAACCATAACACGTACTACCACATATACCAGAAAGGACAGGAGACATCCACTAATCCCA
TTGCTTCCATTTTTCCCTGGACCAGAGGATTAGCCCACAGGGCAAAGCTTGATAACAGTAAAAAACGTGGCCTCTTTGCA
AAGGCTTTGGAAGAAGTGTGTATTGAGACCACTGAGGCTGGCTCAAGCTCATTGATGAAGGACTTGGGTATTTGCATTAA
AGATTTACCTAATATGCAATGTTCTGACTACTTGAATACATTTGAATCCATGGGCAAACTTGGAGAAAACGTGAGGATAA
AACTAGCTCAGGTCAAA

Alignment

ORF - retro_ogar_3057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.72 %
• Parental protein coverage: 98.55 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATSDQVTKDAAEAIKKYNVGVKCAT
          SG.SVVEMQ...MT.I.WELIKEKL.FP..ELDLHSYDLGIEN.DATS.QV.KDAAE.IKKYN.GV..AT
Retrocopy SGSSVVEMQ---MT*ITWELIKEKLFFP*MELDLHSYDLGIENCDATSSQVPKDAAEVIKKYNTGV*GAT

Parental  ITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFV
          ITPDEKRVEE.K.KQMWKSPN.TI.NIL.GT.FREAII.KNIP.L.S.WVKPIIIG.HAY.DQYRAT.FV
Retrocopy ITPDEKRVEELKMKQMWKSPNDTILNILSGTIFREAIIFKNIPWLGS*WVKPIIIGHHAYADQYRATNFV

Parental  VPGPGKVEITYTPNDGTQKVTYLVHNFEDGGGVAMGMYNQDKSIQDFAHSSFQMALSKSWPLYLSTKNTI
          VPG.GKVEITYTP.DGTQKVTYLV..FEDGGGVAMGMYNQ.KS..DFAH....MALSK.WPLYLSTKN.I
Retrocopy VPGTGKVEITYTPSDGTQKVTYLVYKFEDGGGVAMGMYNQEKSVKDFAHF-LPMALSKVWPLYLSTKNNI

Parental  LKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGY
          L.K..G..K..F.......................I...VAQAMKSEG.FIW..KNYD.DV.SDS.AQGY
Retrocopy LEK*YGPLKTSFRRCMTSRTNPNLKPRRSDRA*AHINGIVAQAMKSEGSFIWS*KNYDSDVNSDSMAQGY

Parental  GSLGMMTSVLVCPDGKTVEAEAAHGTVTR-HYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELDL
          .SLGMMTSVLVCP.GKTVEAEAAHGT.TR..Y..YQKGQETSTNPIASIF.WTRGLAHRAKLDN.K...L
Retrocopy DSLGMMTSVLVCPHGKTVEAEAAHGTITR<YYHIYQKGQETSTNPIASIFPWTRGLAHRAKLDNSKKRGL

Parental  FAKALEEVCIETIEAG--FMTKDLAICIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK
          FAKALEEVCIET.EAG.....KDL.ICIK.LPN.Q.SDYLNTFE.M.KLGEN..IKLAQ.K
Retrocopy FAKALEEVCIETTEAGSSSLMKDLGICIKDLPNMQCSDYLNTFESMGKLGENVRIKLAQVK

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_3057 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020527	1 retrocopy	retro_btau_1235,
Choloepus hoffmanni	ENSCHOG00000004574	2 retrocopies	retro_chof_2158, retro_chof_897,
Cavia porcellus	ENSCPOG00000013587	1 retrocopy	retro_cpor_1010,
Homo sapiens	ENSG00000138413	1 retrocopy	retro_hsap_3554,
Gorilla gorilla	ENSGGOG00000012619	1 retrocopy	retro_ggor_2400,
Microcebus murinus	ENSMICG00000009797	1 retrocopy	retro_mmur_1364,
Macaca mulatta	ENSMMUG00000016077	1 retrocopy	retro_mmul_1817,
Nomascus leucogenys	ENSNLEG00000007143	3 retrocopies	retro_nleu_1169, retro_nleu_2328, retro_nleu_3117,
Otolemur garnettii	ENSOGAG00000014848	4 retrocopies	retro_ogar_1488, retro_ogar_2270, retro_ogar_2925, retro_ogar_3057 ,
Otolemur garnettii	ENSOGAG00000034936	1 retrocopy	retro_ogar_334,
Pongo abelii	ENSPPYG00000013125	2 retrocopies	retro_pabe_2935, retro_pabe_926,
Pan troglodytes	ENSPTRG00000012865	1 retrocopy	retro_ptro_2415,
Sus scrofa	ENSSSCG00000023264	1 retrocopy	retro_sscr_549,