Sequence
atgc intronic sequence ATGC exonic sequence...atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 3
--atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
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gaaactactatatctaatcgtcatcaattatatgtacttacttttgaggccatttaaatgtgcatcgctcttgatgtcactgtaaat--tgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 2
atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaat-gtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
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ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgtttt-gccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G049088_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------atttgtagttattagta-gaaatacaaatggcgtattcaatagctgttaaactctta-gttatagggactttaatgtgaatgtatttgc------------tgtaac--catgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
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gtaacaaatatttgagtcatcctctttgatacaatatatagttgggtgttcgtgttctgtaatgaacaacagtt-tactcaatacttcgagagaaagttttcttgtgaaatacatgcaggtctctaaagagacaatgtctgttttctgtgtctgcctgcagcttaccccattataatattttgcagGTGAGACTTTGTAGAGAAAAAGCTACATCCAATGTGTATGCAATGAAAAAGCTTAAGAAGTCCGAAATGTTACGAAGAGGGCAG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 3
-atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaa-actcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
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aagtactgataactagctattattctttttctatgaaccaaagcttctgttagtgattttacttggtgtattgatttaatattatttcattt--ctgtccagGTGAGAATTTGTAAAGAAAAATCTACTGGAAGCGTATATGCAATGAAAAAGTTAAAGAAATCCGAGATGCTTCGACGAGGGCAG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 3
----atttgtagt-tattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
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tgaaacctactgcatttctgttgtaacatgcgaggtgtcatggatt-caggggcaatgtcggtgctaggtaagataacttg----tgtctattatgcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ08009 (Selaginella moellendorffii), 3'ss of exon 2
atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
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-----------------------------gtaagtgcattggctttttcgcatggattggtttgtaagttagtgtacaaat-----ctgtga--atgcagGTCCGGCTCTGCAGAGAAAAATCAACAGGATATGTCTATGCCATGAAAAAACTCAAGAAATCGGAGATGCTGCGAAGGGGCCAG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ16108 (Selaginella moellendorffii), 3'ss of exon 2
atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
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-----------------------------gtaagtgcattggctttttcgcatggattggtttgtaagctagtgtacaaat-----ctgtga--atgcagGTCCGGCTCTGCAGAGAGAAATCAACAGGATATGTCTATGCCATGAAAAAACTCAAGAAATCGGAGATGCTGCGAAGGGGCCAGMapped 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|32271608|gb|CD720767.1|CD720767EST: TTGATGACTTTGAACTTTTGACCATTATAGGAAGAGGTGCCTTTGGAGAG GTGAGACTTTGCAGAG
genomic: TTGATGACTTTGAACTTTTGACCATTATAGGAAGAGGTGCCTTTGGAGAGgtttttatct ... aaccatgcagGTGAGACTTTGCAGAG
EST:
gi|110713213|gb|EE088935.1|EE088935EST: TTGATGACTTTGAACTTTTGACCATTATAGGAAGAGGTGCCTTTGGAGAG GTGAGACTTTGCAGAGAAAAAACTACTGGTCATGTGTATGCCATGAAAAAG
genomic: TTGATGACTTTGAACTTTTGACCATTATAGGAAGAGGTGCCTTTGGAGAGgtttttatct ... aaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
ctgtaac putative branch site (score: 3)
ttagttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - -gaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgt