Sequence
atgc intronic sequence ATGC exonic sequence...ctcgaagtttctttgtcaaatttcagctcatgggctctgcttttacgtgaattgtggtcttcaaagaagctttatagctgatctttgggaggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGCACTTCAACACTGCATAAGAAGATTGCATCTGCTCGCCATGATTTTATCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g08930.1 (Oryza sativa), 3'ss of exon 4
-------ctcgaagtttctttgtcaaatttcagctcatgggct-ctgcttttacgtgaattgtggtcttcaaagaagctttatagctgatctttgggaggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGCACTTCAACACTGCATAAGAAGATTGCATCTGCTCGCCATGATTTTATCA
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actgatactcaa---tactttatgacctttttaaaaatgaaatattatctgctcatgcattttagacttttaacatcttttct---tgaccactggtt--tactacagGCAGTACAAAAGCTGATAGATGAGGAATTTGAAGGTATTGTTCATTTACGGACAACAACCTTTCAAAAAAGAGTTGCAACTGCACGGCATGACTTCATCA
upper sequence: Vv18s0001g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G175867_T02 (Zea mays), 3'ss of exon 4
---------ctcgaagtttctttgtcaa-atttcagctcatgggctctgcttttacgtgaattgtggtcttcaaagaagctttatagctgatctttgggaggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGCACTTCAACACTGCATAAGAAGATTGCATCTGCTCGCCATGATTTTATCA
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ttttgatctcttcagttttgagtactgatacttcagatataaaatcttgttttattatttgtttttgtgtattttgaatccttatac----tcttt------tactgcagGCTGTGCAAAAGTTGATTGATGAGGAATTTGAAGGTATTGTCCATTTGCGGACATCATCATTTCAAAAGAGAGTTTCAACAGCACGGCATGACTTTATCA
upper sequence: Vv18s0001g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G08550.1 (Glycine max), 3'ss of exon 4
---------ctcgaagtttctttgtcaaatttcagctcatgggctctgcttttacgtgaattgtggtcttcaaagaagctttatagctgatctttgggaggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGCACTTCAACACTGCATAAGAAGATTGCATCTGCTCGCCATGATTTTATCA
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tttctgaactctggacaatctctgttacatataaatgtaacacatttttcatta--tcaattttga----caatgaacttccagtgttgacttctgag---tctttcagGCTGTGCAAAATCTGATTGATGAGGAGTTTCTAGGCATTGTTCATCTGCGCACGTCAACATTGCATAAAAAGATTTCTTCTGCTCGTCATGATTTTATTA
upper sequence: Vv18s0001g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G09730.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------ctcgaagt-ttctttgtcaa-atttcagctcatgggctctgcttttacgtgaattgtggtcttcaaaga--agctttatagctgatctttgggaggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGCACTTCAACACTGCATAAGAAGATTGCATCTGCTCGCCATGATTTTATCA
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gtatgcacatgttcattgggctcaatattacacacttgcaccattctttgctattatcatgatttataaatt-tgttgctccatgcatcttgaacttcagatattaaggtagtgaatgaaatt---gtgagttttcagGCTGTTCAGAAGTTAGTCGATGAGGAGTTTCAAGGGATAGAGCATTTGCGTACATCAACACTGCATAAAAAGATAGCAAACGCTCGCCATGACTTCATCAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|294966179|gb|GW839402.1|GW839402EST: CTGATGATCAAGGATTTCAAACTGTTTTGGTCACTGCGACAATGACAAAG GCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGC
genomic: CTGATGATCAAGGATTTCAAACTGTTTTGGTCACTGCGACAATGACAAAGgtatcgtaag ... ggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGC
EST:
gi|110689560|gb|EE065889.1|EE065889EST: CTGATGATCAAGGATTTCAAACTGTTTTGGTCACTGCGACAATGACAAAG GCAGTGCAAAAGCTGATTGATGAGGAGTTTCAGGGAATAGTACATTTGCGC
genomic: CTGATGATCAAGGATTTCAAACTGTTTTGGTCACTGCGACAATGACAAAGgtatcgtaag ... ggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtgaattgtggtcttcaaagaagctttatagctgatctttgggaggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGCACTTCAACACTGCATAAGAAGATTGCATCTGCTCGCCATGATTTTATCA
agctgat putative branch site (score: 4)
tttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcgaagtttctttgtcaaatttcagctcatgggctctgcttttacgtgaattgtggtcttcaaagaagctttatagctgatctttgggaggttttgcagGCAGTGCAAAAGCTGATTGATGAGGAATTTCAGGGAATAGTACATTTGCGCACTTCAACACTGCATAAGAAGATTGCATCTGCTCGCCATGATTTTATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - -ttcagct
- - - - - - - - - - - - - - catgggc
- - - - - - - - - - - - - - - - - - ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaag