Sequence
atgc intronic sequence ATGC exonic sequencegttagtagtcagtgaatgatgactcttaactccaacttatggaattttctgctccaatacatgatagcaatgagttatatgcactggtagatacacatacatgaaaatatatcctagcaatgagttatatgctatacgcattaaaacatacaggttaaaaatatctaatggttggatgttagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAAAAGAGGGAAT
Basic information
species | Glycine max |
transcript | GLYMA06G11920.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 5
gttagtagtcagtgaatgatgactcttaactccaacttatggaattttctgctccaatacatgatagcaatgagttatatgcactggtagatacacatacatgaaaatatatcctagcaatgagttatatgctatacgcattaaaacatacaggttaaaaatatctaatggttggatgttagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAAAAGAGGGAAT
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-----------gtaagaaaagac----agct-----ttacatgaactttcatttctgcatgcttccgcatttatttct-----------gaagtcttcagatgaaaatttgcc--aacagagagaagt-tgcgaaa-gtagtat----ttcagtttttttttgttttca---taaccttcagGTTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCATCCACAAAGATGCTCAACGTGCGCATCCGGTCATTACCATGCTTTGAGCAAGAAGGAAT
upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 5
gttagtagtcagtgaatgatgactcttaactccaacttatggaattttctgctccaatacatgatagcaatgagttatatgcactggtagatacacatacatgaaaatatatcc-tagcaatgagttatatgctatacgcattaaaacatacag-gttaaaaatatctaatggttggatgttagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAAAAGAGGGAAT
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-----------------------------------------------------------------------------------caaagaattactctttttttaaagtcttcccatgatcataatgttcccaataaa-gtggtagtgcaagtaatatttctgatttccttttcatacccttcagGGTGGGAGTATTCAACTGATGGAAAATGTGAGAAAATGCCAGCCACGAAGTTGCTCAATGTGCGCATCCGGTCATTGCCATGCTTTGAGCAAGAAGGCAT
upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 4
gttagtagtcagtgaatgatgactcttaactccaacttatggaattttctgctccaatacatgatagcaatgagttatatgcactggtagatacacatacatgaaaatatatcctagcaatgagttatatgctatacgcattaaaacatacaggttaaaaatatc-taatggttggatgttagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAAAAGAGGGAAT
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------------------------------------------gttagtaagagggaaaggaaataagcaaaagtttacctgttttgcta-ataagaacagatgacaa-atcaattagtaatgcataaagta--aaaaatatttgtttgctcatgtggaaatttttgtgatggatgaacttcagGGTGGGAGTACTCAACAGATGGGAAATGCGAGAAAATGCCGTCAACACGATTGCTTAATGTAAAAATAAAATCATTGCCGTGTTTAGAGCAAGAGGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgctatacgcattaaaacatacaggttaaaaatatctaatggttggatgttagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAAAAGAGGGAAT
atctaat putative branch site (score: 3)
ttaaaaatatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtagtcagtgaatgatgactcttaactccaacttatggaattttctgctccaatacatgatagcaatgagttatatgcactggtagatacacatacatgaaaatatatcctagcaatgagttatatgctatacgcattaaaacatacaggttaaaaatatctaatggttggatgttagGCTGGGAATATACTACTGATGGAAAATGTGAGAAAATGCCATCTACTCGACTGCTAAATGTGAAGATAAAGTCATTGCCATGTTTTGAAAAAGAGGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG