Sequence
atgc intronic sequence ATGC exonic sequence...ggaagctaaaatgtttttaccaattggattaaggtcacatggatcacatgcctgcttcattttatgtatattatctaattggcatagtacatgcttgtagGGTTTGGTACATGTAGCAAGGAAGATGCCCAAAAATGCTCATGCTCATTTTATACTTGGATTAATGTATCAGAGGTTGGGTCAGCCACAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g09890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g67920.2 (Oryza sativa), 3'ss of exon 2
--------ggaagctaaaatgtttttaccaattggattaaggtcacatggat-cacatgcctgcttcattttatgtatattatctaattggcatagtacatgcttgtagGGTTTGGTACATGTAGCAAGGAAGATGCCCAAAAATGCTCATGCTCATTTTATACTTGGATTAATGTATCAGAGGTTGGGTCAGCCACAAAAG
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cctttttttagcattacattatcctaattaatatgcccatggcgatttgaatgcacatagtcagc-------atacgtatcgctaaaaccggatcgtcctt--ttgcagGCTTTGGTACATGTGGCACGGAAGATGCCTAAAAATGCCCATGCACATTTTATGTTGGGTTTGATGTACCAAAGGCTTGGTCAGCCACAGAAG
upper sequence: Vv17s0000g09890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G18330.2 (Glycine max), 3'ss of exon 2
--ggaagctaaaatgtttttaccaattggattaaggtcacatggatcacatgcctgcttcattttatgtatattatctaattgg---catagtacatgcttgtagGGTTTGGTACATGTAGCAAGGAAGATGCCCAAAAATGCTCATGCTCATTTTATACTTGGATTAATGTATCAGAGGTTGGGTCAGCCACAAAAG
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tagtaatttgttatggtcatggtcattg--ttggtgttactgttactat-tattggctttattg-gtat-taccaacaaaataagtccatgctaatatgttatagGGCTTGGTTCATGTTGCAAGGAAGATGCCCAAAAATGCTCACGCTCATTTTATACTCGGCTTGATGTACCAAAGATTAAGCCAACCTCAAAAG
upper sequence: Vv17s0000g09890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G36580.1 (Glycine max), 3'ss of exon 2
ggaagctaa-aatgtttttaccaattggattaaggtcacatggatcacatgcctgcttcattttatgtatattatctaattggcatagtacatgcttgtagGGTTTGGTACATGTAGCAAGGAAGATGCCCAAAAATGCTCATGCTCATTTTATACTTGGATTAATGTATCAGAGGTTGGGTCAGCCACAAAAG
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gatcattgttggtgttgctgttactattattggctttattgctattgt-tgtagtttttgttttattaccaacaaaataagtccatgttaatatgttatagGGCTTGGTTCATGTTGCAAGGAAGATGCCCAAAAATGCTCACGCTCATTTTATACTCGGCTTGATGTACCAAAGATTAAGCCAACCTCAAAAG
upper sequence: Vv17s0000g09890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G63200.1 (Arabidopsis thaliana), 3'ss of exon 2
-------ggaagctaaaatgtttttaccaattggattaaggtcacatggatcacatgcctgcttcattttatgtatattatctaattggcatagtacatgcttgtagGGTTTGGTACATGTAGCAAGGAAGATGCCCAAAAATGCTCATGCTCATTTTATACTTGGATTAATGTATCAGAGGTTGGGTCAGCCACAAAAG
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gtcctcttatattcataatgctcttcgcagttgattattggtctaat---tttcatgatgatgatgctctatataaatt--ctgattttcct--tctctgcttatagGGTTTGATTCATGTTGCAAGGAAGATGCCCAAAAATGCTCATGCCCATTTTATACTTGGTCTTATGTTTCAACGATTGGGCCAATCTCAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgcctgcttcattttatgtatattatctaattggcatagtacatgcttgtagGGTTTGGTACATGTAGCAAGGAAGATGCCCAAAAATGCTCATGCTCATTTTATACTTGGATTAATGTATCAGAGGTTGGGTCAGCCACAAAAG
atctaat putative branch site (score: 3)
ttcattttatgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaagctaaaatgtttttaccaattggattaaggtcacatggatcacatgcctgcttcattttatgtatattatctaattggcatagtacatgcttgtagGGTTTGGTACATGTAGCAAGGAAGATGCCCAAAAATGCTCATGCTCATTTTATACTTGGATTAATGTATCAGAGGTTGGGTCAGCCACAAAAG
- - - taaaatg
- - - - - - - - - - - - - - - - - tcacatg
- - - - - - - - - - - - - - - - - - - - - - cacatgc