Sequence
atgc intronic sequence ATGC exonic sequencegtaatacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgactaatcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
Basic information
species | Glycine max |
transcript | GLYMA12G01360.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G01360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G028812_T01 (Zea mays), 3'ss of exon 5
gtaatacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgac-taatcacagcaga---atccat--ttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
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gtg-tgcacgcatgcaacaattcctcattttcttgtcagatagctatcaggactcaggat--gtgggggtgacacagtcacgactgatgaatgaatggttcagGAAGCGCCCCCCTGACCATCGTGCAGCTGCTGTGGGTGAACCTGATCATGGACACCCTGGGCGCCCTGGCGCTGGCGACGGAGCCCCCCAACGACGCCAT
upper sequence: GLYMA12G01360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G476000_T01 (Zea mays), 3'ss of exon 5
gtaatacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgactaatcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
|| | | | ||| | | || | | || || | || || | || | | ||| ||| |||| || ||||| || || ||| |||| ||||| ||| |||||||||||||||||||||| |||| ||||| || || || || | || | | |
-------------gtattctcgtcatcagatagtcttgtttctttctgcgacatacagct-------gacgaatggacaaatgaaaatgaatt-cagGGAGCGCCCCTCTGACCATCGTGCAACTGCTGTGGGTGAACCTGATCATGGACACCCTGGGCGCCCTGGCGCTGGCGACGGAGCCCCCCAACGACGCGAT
upper sequence: GLYMA12G01360.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgactaatcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
||| ||| | | | | | || || |||||| | |||| ||| || ||| ||| | || | | | || || |||| |||||||| || |||||||| ||| |||||||||| ||||||||||||||||| || || |||||||| || || ||||||||||| |||| || |
gtacgacagaaaa--accaatcaaacaccatctttc----ttctagc-----gtttggtcaaatatag-taaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
upper sequence: GLYMA12G01360.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G57330.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgactaatcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
|| || | || | || || || | | || | |||| |||| | |||| | | ||| || ||||||| ||||| || || || || || ||| |||||||||| ||||||||||||||||| || || |||||||| || || || |||||||| | || || |
---gtaagtaaaatcaaacacatgc-acaattttcaccaatgatttttgaataacagtttcagt---aatgattgtttt--gca----ccttttcagGATCTGCGCCACTCACCGCAGTGCAACTGCTTTGGGTGAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCGACCGAACCTCCCAACGAAGGTTT
upper sequence: GLYMA12G01360.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 5
gta-atacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgactaa-----tcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
|| | ||| || || |||| || || || | | | | || | ||| |||||||| | | | | | ||||||| |||||||||||||||||||| || |||| ||||| || |||||||||||||| || || ||||| || |||||||||| |||| |||||| ||
gtgcgttcatccattaaatctttt-------tccttacaacttaagatttggcgtcta-tataataaagatgacttagaaatttctttccaagtaattttcagGATCTGCTCCTCTTACTGCTGTCCAGTTGCTCTGGGTGAATATGATCATGGACACTCTTGGTGCATTAGCCTTGGCTACAGAGGCTCCAACTGATGGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagctaaatatttagttcaatttagatgactaatcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
gactaat putative branch site (score: 2)
tccatttc putative PPT
taaatatttagttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgactaatcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC