Sequence
atgc intronic sequence ATGC exonic sequencegtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgtcaaattttctcaaaaaccatgttactgaagtaattgagcctacttatcttatactgattctaaataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
Basic information
species | Glycine max |
transcript | GLYMA02G44000.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44000.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgtcaaattttctcaaaaaccatgttactgaagtaattgagcctacttatcttatactgattctaaataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
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------------------------------------------------------------------------------------------------gtaaagctctatatattaaagaatagctcttcttagcttact-----tacaaattgtgaaataattc-acttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
upper sequence: GLYMA02G44000.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27150.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgtcaaattttctcaaaaaccatgttactgaagtaattgagcctacttatcttatactgattcta-aataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
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------------------------------------------------------------------------------------------------------------------gcaagtcactatgg-gaaacacttctttctttatat-ttgaatcaatcaaacaataatgtgattctacttgcagGTGGAAGTGGACCTTGTGACAGGAAAAACCGAGATTTTAAGATCCGATATTATTTATGACTGTGGAAAGAGTCTTAATCCTGCAGTTGATTTAGGACAG
upper sequence: GLYMA02G44000.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 6
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatg--tcaaattttctcaaaaaccatgttactgaagtaattgagcctactt-atcttatactgattctaaataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
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----------------------------------------------------------------------------------------attaagttagtattcttcaggtaaacttggaggagactaggctttcatgcttaaccatgcttcaatttttacta--taataatgaaacattgggtgtcacagGTGGAGGTAAATCTTCTCACTGGACAAACCACAATTTTGCAATCTGATATTATATATGACTGTGGTCAGAGTCTCAACCCTGCTGTGGATTTAGGACAG
upper sequence: GLYMA02G44000.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 3'ss of exon 6
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgt-caaattttctcaaaaacca-tgttactgaagtaattgagcctactt-atcttatactgattctaaataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
||| | | |||| || || || ||||||| | ||| | || || | || | || | | || | || | | | | || | || | | | || | || |||| || |||| | | | | || ||||||||| | ||||||| | ||||||||||| | |||||||| | || ||||| ||||| ||||| || || || ||||||||||| ||||||||||||
-----------------------------gcaagtttt---tcaagattac-cttaatcgctttcattagt----gcttttgttaaaattaaattagtattcttcaggtaaacttggaggagactatagcttccatgcttaaacatgctccaagttttact-atactaattta-actttgggtgtcacagGTGGAAGTAAATCTTCTCACTGGAGAAACCACAATTTTGCAATCTGATATTATATATGACTGTGGGCAAAGCCTCAACCCTGCTGTGGATTTAGGACAG
upper sequence: GLYMA02G44000.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgtcaaattttctcaaaaaccatgttactgaagtaattgagcctacttat-cttatactgattcta-aataatggaattt---atttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
||| | | |||| || ||| || | ||| | | || | ||||| |||||| || | | || ||| | | | | | || || || ||| | | | ||| ||||||| || || | || |||||||| | ||||||| | |||| |||||| | |||||||| | || ||||| ||||| ||||| |||||||| ||||||||||| ||||||||||||
-----------------------------gcaagtttt---tcaagatcccattaattcctctccat-----agagtttttattgaa-attaagt--tagtattc--ttcaggtaaacatggaggagagtaggctttcatgcttaaccatgcttcaatttttactataataatgaaactttgggtgtcacagGTGGAGGTAAATCTTCTCACTGGACAAACCACAATTTTGCAATCTGATATTATATATGACTGTGGTCAGAGTCTCAACCCTGCTGTGGATTTAGGACAG
upper sequence: GLYMA02G44000.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaa-atggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgtcaaattttctcaaaaaccatgttactgaagtaattgagcctacttatc-ttatactgattctaaataatggaattt---atttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
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-----------gcaagttttttgagat-tgcctaaaccactttaattattgtttttgttggagttaaattagtgctcttcatgttaacttggagaagactaagcttgcaggcttaatgatgcatcaaattttactatcaaggccgatatatagttatgtgtgtgctaa-taatgaaactttgagtgtcacagGTGGAGGTAAATCTTCTCACTGGAGAAACCACCATTTTGCAATCTGATATTATATATGACTGTGGGCAGAGCCTCAACCCTGCTGTGGATTTAGGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaattgagcctacttatcttatactgattctaaataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
ttctaaa putative branch site (score: 2)
tttatttctc putative PPT
attctaaataatggaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgtcaaattttctcaaaaaccatgttactgaagtaattgagcctacttatcttatactgattctaaataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT