Sequence
atgc intronic sequence ATGC exonic sequence...ggtgattttgtcatgagatagaggcaaatcagcagtttaccatgctatgcacccaaaatatattctttccaaccctatgttgatgctaaaatcttttcagGTCTTAGTTCTTCTTTTGTTAACGTCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGATTAGATAGTAATCTAGATG
Basic information
species | Glycine max |
transcript | GLYMA01G08200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G08200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G433942_T01 (Zea mays), 3'ss of exon 2
--------ggtgattttgtcatgagatagaggcaaatcagcagtttaccatgctatgcacccaaaatatattctttccaaccctatgttgatgctaaaat-cttttcagGTCTTAGTTCTTCTTTTGTTAACGTCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGATTAGATAGTAATCTAGATG
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atacataaaaaaattttatctgaagtcatgatcatgctggtaa------agagaatatatacaaaacataccctct---aacttgtttaagcattatgccacctttcagGATCTGAGTCTTCTGCTTCTAACTTCTGGGAGAGATCCAGGGATCATACCTCGCAATGCACATCCTCCAGAACCCGAAGGGTTTGATGGCAATGCAGAGG
upper sequence: GLYMA01G08200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
ggtgattttgtcatgagatagaggcaaatcagcagtttaccatgctatgcacccaaaatatattctttccaaccctatgttgatgctaaaatc----ttttcagGTCTTAGTTCTTCTTTTGTTAACGTCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGATTAGATAGTAATCTAGATG
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----atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgcacccaaaatatattctttccaaccctatgttgatgctaaaatcttttcagGTCTTAGTTCTTCTTTTGTTAACGTCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGATTAGATAGTAATCTAGATG
tgctaaa putative branch site (score: 2)
tcttttc CT-rich tract
aaaatatattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtgattttgtcatgagatagaggcaaatcagcagtttaccatgctatgcacccaaaatatattctttccaaccctatgttgatgctaaaatcttttcagGTCTTAGTTCTTCTTTTGTTAACGTCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGATTAGATAGTAATCTAGATG
ggtgatt
- - - - - tcatgag
- - - - - - - - - - - - - - - - - - - -ccatgct
- - - - - - - - - - - - - - - - - - - - - - - - - -cccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct