Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgttgctttttgttgcaccaaatcagttaattgtatttgcttgtctttggatgatggagcttggttgcttttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTTTTCAAAGTTTTTGCTGGTGGAAAGCCG
Basic information
species | Glycine max |
transcript | GLYMA17G34690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G33010.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtgttgctt--tttgttgcaccaaatcagttaattgtat----ttgcttgtctttggatgatggagcttggttgctt--ttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTTTTCAAAGTTTTTGCTGGTGGAAAGCCG
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gtgagtctcctttgctttggcctttcaaggtttttactctcatagcatcatacagatttgaatatttggatatgattacttaattcagATTACTGCTTCCTTTGACGAAACAACCACCTTGGATGATGTCGATAAACTTTTCAAAGTTTTTGCTTCTGGCAAGCCT
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------gtgagtgttgctttttgt-tgcaccaaatcagttaattgtatttgcttgtc--tttggatgatggagcttggttgcttttca-gATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTTTTCAAAGTTTTTGCTGGTGGAAAGCCG
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gtgagtttcttcatatatatatatatatatatatatatatatatatttcttcaat-atctggatatgattattaacattgatgggttttttttcttgttctttaagATTACTGTTGCTTTCGATGAAACAACCACCTTGGATGATGTCGATAAACTTTTTGAAGTTTTTGCTTCGGGCAAGCCC
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtgttgctttttgttgcaccaaatcagttaattgtatttgcttgtctttggat---gatggagcttggttgcttttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTTTTCAAAGTTTTTGCTGGTGGAAAGCCG
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gtgagtgtt-ctacatgtt-tgttcaattggttaattatgatctttcatcatgagattttattggagcttggttgcctttcagATCACTGTTTCCTTTGATGAAACAACAACAATAGAGGATGTGGACAAGCTTTTCAAAGTTTTTGCATGTGGCAAGCCT
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtgttgctttttg-ttgcaccaaatcagttaattgt-atttgcttgtctttggatgatggagcttggttg--cttttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTTTTCAAAGTTTTTGCTGGTGGAAAGCCG
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gtgagtctgttgtagtgattgattttgtttggtaaattattattcttctatatgtcaaatatgattcgaatttggacctgtcagATAACTGTTTCTTTTGATGAGACAACAACATTAGAGGATGTGGACAAGCTTTTCAAAGTGTTCTCTTGTGGCAAGCCAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|17400446|gb|BM177228.1|BM177228EST: ATGCTGCTCTCAAGAGTGGAATAAATTTGCGAGTTGTAGATGGAAACACT ATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTT
genomic: ATGCTGCTCTCAAGAGTGGAATAAATTTGCGAGTTGTAGATGGAAACACTgtgagtgttg ... tgcttttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTT
EST:
gi|23064257|gb|BU579030.1|BU579030EST: CTGCTCTCAAGAGTGGAATAAATTTGCGAGTTGTAGATGGAAACACT ATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTT
genomic: CTGCTCTCAAGAGTGGAATAAATTTGCGAGTTGTAGATGGAAACACTgtgagtgttg ... tgcttttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcagttaattgtatttgcttgtctttggatgatggagcttggttgcttttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTTTTCAAAGTTTTTGCTGGTGGAAAGCCG
agttaat putative branch site (score: 4)
ttgcttttc putative PPT
ttaattgtattt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgttgctttttgttgcaccaaatcagttaattgtatttgcttgtctttggatgatggagcttggttgcttttcagATCACTGTTGCTTTTGATGAAACAACCACATTAGAGGATGTTGATAATCTTTTCAAAGTTTTTGCTGGTGGAAAGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA