RetrogeneDB ID: retro_tbel_3930

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_40454:10..715(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI1
• Ensembl ID: ENSTBEG00000012540
• Aliases: None
• Description: GDP dissociation inhibitor 1 [Source:HGNC Symbol;Acc:4226]

Sequence

>retro_tbel_3930
GGAGAGGACTGGAACACTGACTTAATTCCCAAGTTCCTTATGGCTAGTGGTCAGCTGGTTAAGATGCTGCTTTATACAGA
GGCTACTCGTTACCTGGATTTCAAAGTGACCGTAGGGAGCTTTGTCTGTAAGGGAGGAAAAATCTATAAGGTTCCTTCCA
CTGAAGCCGAAGCCCTAGCATCTAGCTTAATGGGACTATTTGAAAAACATCGCTTCCTAGTGTATATTGCCAACTTTGAT
GAAAAAGATTCTAGAACTTTTGAGGGCATTGATCCTAAGAAGACTTCAATGCGAGATGTGTACAAGAAATTTGATTTGGG
CCAAGATGTAGTATATTTTACTGGTCGGCCTCTTGCAATTTACCAAAATGGTGACTACTTAGATCAACCATGTTGTGAAA
CCATTAATAGGATTAAACTTTACAGTGAGTCCTTGGCAAGCTATGGTAAAAGCCCATACCTTTATCCACTCTATGGCCTT
GGAGAACTGCCACAAGGATTTGCAAGGCTAAGTGCTATTCATGGAGGTACCTACATGCTCAATAAACCAATTGAAGAAAT
CATTGTGCAGGATGGAAAAGTTATTGGTGTAAAATCTGAAGGAGAGATTGCTTGCTGTAAACAGCTCATTTGTGACCCCA
GCTATGTCAAGGATCAGGTAGAAAAAGTGGGTAATCTGTGTCATCTGCATCCTCAACTACCCCAT

Alignment

ORF - retro_tbel_3930 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.63 %
• Parental protein coverage: 55.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVPSTETEALASNLMGMFEKR
          G.DWN.DLIPKFLMA.GQLVKMLLYTE.TRYLDFKV..GSFV.KGGKIYKVPSTE.EALAS.LMG.FEK.
Retrocopy GEDWNTDLIPKFLMASGQLVKMLLYTEATRYLDFKVTVGSFVCKGGKIYKVPSTEAEALASSLMGLFEKH

Parental  RFRKFLVFVANFDENDPKTFEGVDPQTTSMRDVYRKFDLGQDVIDFTGHALALYRXXXYLDQPCLETINR
          R...FLV..ANFDE.D..TFEG.DP..TSMRDVY.KFDLGQDV..FTG..LA.Y....YLDQPC.ETINR
Retrocopy R---FLVYIANFDEKDSRTFEGIDPKKTSMRDVYKKFDLGQDVVYFTGRPLAIYQNGDYLDQPCCETINR

Parental  IKLYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCK
          IKLYSESLA.YGKSPYLYPLYGLGELPQGFARLSAI.GGTYMLNKP...II...GKV.GVKSEGE.A.CK
Retrocopy IKLYSESLASYGKSPYLYPLYGLGELPQGFARLSAIHGGTYMLNKPIEEIIVQDGKVIGVKSEGEIACCK

Parental  QLICDPSYIPDRVRKAGQVVRIICILSH
          QLICDPSY..D.V.K.G........L.H
Retrocopy QLICDPSYVKDQVEKVGNLCHLHPQLPH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3930 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3930 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010921	4 retrocopies	retro_meug_1228, retro_meug_2135, retro_meug_561, retro_meug_795,
Microcebus murinus	ENSMICG00000016418	1 retrocopy	retro_mmur_1095,
Sarcophilus harrisii	ENSSHAG00000005650	1 retrocopy	retro_shar_43,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,
Tupaia belangeri	ENSTBEG00000012540	4 retrocopies	retro_tbel_1832, retro_tbel_2262, retro_tbel_2457, retro_tbel_3930 ,
Tursiops truncatus	ENSTTRG00000011454	1 retrocopy	retro_ttru_1205,