Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttaacctcctgtcgtttactactatggcattcaacacatacacattcttgttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20190.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 3'ss of exon 9
---------gtaagctta--acctcctgtcgtttactactatggcat-tcaacac--atacacattcttgttaatattggtatatgg------taatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
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tttattccggtaaccatagaagctgtttcagtgttttgcaacagtaagtcagtactcttatacttcctcagtagggctaacatactgatcaaattatcagGTACTTTTCAAGCTTGTTGTGATAACTGTGCTTGTTATTGCTGAATCCGCCGACAACTGCATAAAAACT
upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 8
gtaagcttaacctcctgtcgtttactactatggcattcaacacatacacattcttgttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
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gtaagttcgcctagttatctcggatt--tatcacaattttgatgcttttgaaattattaatttttg-atctgataatcagGTCCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAGTCTGCAGATAACTGCATTAAAACG
upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 8
gtaagcttaacctcctgtcgtttactactatggcattcaacacatacacattcttgttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
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gtaagtt---ctcctagtatctcggatttatcacaattttgatgcttttgaaattattaatttttg-atctgataatcagGTCCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAGTCTGCAGATAACTGCATTAAAACG
upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 8
gtaagcttaacctcctgtcgtttactactatggcattc-aacacatacacattcttg-----ttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
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gtaagttctactactttttgtctatgataatcatgttttggtttttggatgtatctgaactcttgatacttg-atctgataatcagGTCCTTTTGAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCGGACAACTGCATAAAAATG
upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 8
gtaagcttaacctcctgtcgtttactactatggcattcaacacatacacattcttg-----ttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
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gtaagttttactttttatctatggtaatcatgt--tttggtttttggatgtttctaaaatcttaatacttg-atctgataatcagGTCCTTCTGAAGCTGGTTGTGATTACTGTGCTTGTAATTGCGGAATCTGCAGATAACTGCATAAAAACG
upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
gtaagcttaacctcctgtcgttt-actactatggcattcaacacatacacattcttgttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
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gtaagttcatctttcttctttctgaatattgcagtgtccaa------tgttccctctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactatggcattcaacacatacacattcttgttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
tgttaat putative branch site (score: 3)
attcttgttaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttaacctcctgtcgtttactactatggcattcaacacatacacattcttgttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT