Sequence
atgc intronic sequence ATGC exonic sequence...cccgctgtgttgttttgaattttgtataaaggcttgttttaatattatgtgggtattcttctttttctttctgttctaatcattgcatttcatattttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 7
----------------------------------------cccgctgtgttgttttgaattttgtataaaggcttgttttaatattatgtgggtattcttct----ttttctttctg-ttctaatcattg-----catttcatattttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
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gtaagtaccatttgttttctgctgggaattttaaacagatgctgaaggaagacgtttaactcaaaattatgggccttattatgttttcataaattgtctttcgaaattctcatgatgattgcaatgattcaagtttatttcctttcacagATAGCGTTAGAGAGGGATAATGTCAGCAATGATCCCAAGTCCATCATGCCTGCGGCATTTGTTTCGTTTAAAACACGATGGGGTGCTGCAGTTTGTGCAC
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G16230.2 (Glycine max), 3'ss of exon 2
cccgctgtgttgttttgaattttgtataaaggcttgttttaat---attatgtgggtattcttctttttctttctgttctaatcattgcatttcatattttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
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---atcagcataataggtcctttgtaaatagccatattgtgatttcattgcttttgttttctttctttaagaattatcttgatggtcagaggtgattttgcagATTGTTGAGGAGAGGGAAAATGTCACAAATGATCCCAAGGCCATCATGCCCGCTGCATTTGTTTCATTTAAAACAAGATGGGCTGCTGCTGTTTGTGCAC
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------cccgctgtgttgttttgaattttgtataaaggcttgttttaa--tattatgtgggtat---tcttctttt-------tctttctg-ttctaatcattg-----catttcatattttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
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gtaagtaccatttattttctgctaggagttttaaacatatgcggaaggaagtcgtttaactcaaaatttcactaaggataatatctgcagatattatgggacttattatgttttcataaattgtcttttgaaagtctcatgatgattgcaatgattcaagtttatttcctttcacagATAGCGTTAGAGAGGGATAATGTCAGCAATGATCCCAAGTCCATCATGCCTGCTGCATTTGTTTCGTTTAAAACACGATGGGGTGCTGCAGTCTGTGCAC
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G10490.1 (Glycine max), 3'ss of exon 7
cccgctgtgttgttttgaattttgtataaaggcttgttttaat---attatgtgggtattcttctttttctttctgttctaatcattgcatttcatattttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
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--atttgcatagtaggtcattt-gtaaatagccatattttgatttcattgcttttgttttctttctttaagaattctcttgatggtcagaggtgattttgcagATTGTTGAGGAGAGGGAAAATGTCACAAATGATCCCAAGGCCATCATGCCTGCTGCATTTGTTTCATTTAAAACAAGATGGGCTGCTGCTGTTTGTGCAC
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S13_374V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------cccgctgtgttgttttgaattttgtataaaggcttgttttaatattatgtgggtattcttctttttctttctgttctaatcattgc---atttcatat-tttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
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gtaagctgaaaacatattccttccatcttttggagtatggtgcaa--tctatttatcacatcgtttgggtccagctctgcgccagtgttcactaagaattgcttggttgggtctatccagGCAGAAATCGAGCGTGAATTTGTGATAAGCGACCCAAAGGCCATAATGCCGGCAGCGTTTGTTTCCTTCAGAACCCGCTGGGGGGCTGCTGTTTGCGCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtgggtattcttctttttctttctgttctaatcattgcatttcatattttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
ttctaat putative branch site (score: 2)
atttcatatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccgctgtgttgttttgaattttgtataaaggcttgttttaatattatgtgggtattcttctttttctttctgttctaatcattgcatttcatattttagATATCTGTGGAGAGAGAAAGGGTTGCAAATGATCCTAAGTCTATCATGCCCGCAGCATTTGTTTCCTTCAAAACTCGGTGGGGTGCTGCTGTTTGTGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-ccgctgt
- - - - - - - - - - - - -ataaagg