Sequence
atgc intronic sequence ATGC exonic sequence...tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgtaatcattaaggttaattaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
Basic information
species | Glycine max |
transcript | GLYMA02G07940.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 9
---------tacttgagtggttcgaaattcatttacatttacaat-tatgttaacccacttcatgtaatcattaagg--ttaattaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
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gtaagttactgcacaatctccctgtgctaaattcagagtaaaaatgtaaagcagtcaggttaagcaagagactgatgcatgaagctgctgctg-ttcttgtggtttgttcagAACATTCAGGGTTTCATGTGGGACGAGGAGAAGGTGAACAATGAGCTGAAGACCTACATGACCCGTGGGTTCAGGGATGTGAAGGAGATGTGCAGGAGCC
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgtaa--tcattaaggttaattaaatgatgattattatgta-atgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
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------------gtaagactcg---aaaatcaagactgtatgacctaatcgaatctaaagccactc-gatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgta-atcattaaggttaattaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
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-------gtatgtatgagtctctcaacaacttacctttgacagaccaagtactcgaacaaaaccgattttgatcagattagttgtttccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
---tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgtaatcattaaggtta-attaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
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tgatgctagagctgtaatgaat--gttgaattttataa--aaactgacaatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccacttcatgtaatcattaaggttaattaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
ggttaat putative branch site (score: 4)
taatcattaaggttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgtaatcattaaggttaattaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -ttgagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat