Sequence
atgc intronic sequence ATGC exonic sequence...taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g56320.1 (Oryza sativa), 3'ss of exon 4
taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacatt-ttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
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--------------------gtaagtccattacctttttctgcggagacatataagatccactttattcccaaatgttaatgacaa---attaatttccagCATTGCTGTCTATAAAGCTCTGTACAAAAGCTTTGGAGGGTTTGCTGCTGATGTAGTAGCTGCAATAGATCAG
upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 4
--taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
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cccatagaatgtgctatccccatagtattaa-gtattcaacttcccatgacttttaaaagaaaaataat-ttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G21920.1 (Glycine max), 3'ss of exon 4
taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttc---------tggca--ttaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
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-----------gtctgattttgttttttaattatttcatttaaccttgtatagtttcctttttaaaaaaaaatagtaatttaagttagtgctgcatttcaatcttttacagCATTGCTGTTTACAAGGCATTATACAAGAGCTTTGGTGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G30460.1 (Glycine max), 3'ss of exon 4
taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
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tctgttctaacctggatttctaataattacatgcaagcataattaatttttattctatatatgtaaacatttgaatgcattccatttcaatcttttacagCATTGCCATTTACAAGGCACTATACAAGAGATTTGGAGGATTTGCAGCAGATGTTGTTGCAGCTATTGACCAG
upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G13590.1 (Glycine max), 3'ss of exon 4
-taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
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atctgttctaacctggatttctaataactacatgcaagcataattattttttattctatgtatgcaacatttga-atgcattccatttcaatcttttacagCATTGCCATTTACAAGGCACTATACAAGAGATTTGGAGGATTTGCAGCGGATGTTGTTGCAGCTATTGACCAG
upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 4
-taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
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gtaagtaaatagacattagccagatatca------tctttttat---cattcatattgcattgagtgtactaatgac-----attttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G44530.1 (Arabidopsis thaliana), 3'ss of exon 4
-taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
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gtaagtaaaataataa--gacttagatcaatgt-cgaaatctatacaaaactaacttaaacttttatgtttttgaact-------------ttgttttcagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGAGGTTTTGCTGCAGATGTTGTAGCAGCTATAGATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
cactaac putative branch site (score: 1)
tattctattcttttcc putative PPT
tatattctattctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - -aaaaaaa
- - - - - - - - - -ctcatgt
- - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactaac