Sequence
atgc intronic sequence ATGC exonic sequence...acttttatatgggtggtatagctgcttttgttttcttatgtgttgaggaccttgtggttgtattgtatcctttgactcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 2
acttttatatgggtggtatagctgcttttgttttcttatgtgttgaggaccttgtggttgtattgtatcct-ttgactcaaaccacttaat------agagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
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-------tgtgggaaatgtatgagtatgacatattttaagggcagcaaatttcgattcaaaatagcaaaatgttgactgcagtcgctaatttattccatgcatacagGTACTGGTGGAAATCCTAATTTGGGAGAGCAAGCTGCTGAGGAATCAAAAGAAGCCATAGCCAATGCCCTGAAGGATTCTGACCTTGTCTTCATAACGGC
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 2
-acttttatatgggtggtatagctgcttttgttttcttatgtgttgaggaccttgtggttgtattgtatcctttgac-tcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
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gccctataacaatgcatcatcaaaactgtaaatttccattgaa--aatgtttcagaggttggctagattcagtaaatatgatactacgtaacacatgcacagGTGCCGGTGGAAATCCGAATTTGGGAGAGCAGGCTGCTGAGGAATCAAGAGAAACCATAGCCACTGCCCTGAGGGATTCAGATCTTGTCTTCATAACAGC
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 2
---------------------------------------acttttatatgggtggtata---gctgc--ttttgttttct-tatgtgt-tgaggaccttgtggttgtattgtatcctttgactcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
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gtcaggaagttgcattttatgcctagggggttcctttgtacttgattataacatgcatatatgttgcaatcatgtgatctatatgtgtgtgtgtgtggcttcactccaatgtgacctttgattcgagttgcttgatagagatgcagGTACTGGTGGGAATCCACTTTTGGGGGAACAAGCTGCTGAGGAATCAAAAGAAGCTATTGCCAATGCTCTTCAAGGATCAGATTTAGTGTTTGTAACTGC
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------acttttatatg-ggtggtatagctgcttttgttttcttatgtgttgaggaccttgtggttgtattgtatcctttgactcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
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gtcaggcacttgcattttatgcctaggtggttcctttgtgcttgattatgacatgcatatatgttgctatagtgtgatttgtgtgtgcctgtgtggtacttagcttcattctaatgtgtcctttgattcaagttgcttgagagagatgcagGTACTGGAGGGAATCCGCTTTTGGGGGAACAAGCTGCTGAGGAATCAAAAGAAGCTATTGCTAATGCTCTTCAAGGCTCGGATTTAGTGTTTGTAACTGC
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 2
---------------------------acttttatatgggt-ggtatagctgcttttgtttt-cttatgtgttgaggaccttgt--ggttgtattgtatcctttgactcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
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gtcaggcactctacttgcatagtttttactatgatgtgatttgtttttgtggctacagtcttgtttctttgctgaatttgttgacaaattgaggggtggcctttgattcaaattacttgatagagatgcagGTACAGGTGGGAATCCACTTTTGGGGGAACAAGCTGCGGAGGAATCCAGAGATGCTATTGCTGATGCTCTTAAAGGATCAGATTTGGTATTTATAACGGC
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 2
---------------------------acttttatatgggt-ggtatagctgcttttgtttt-cttatgtgttgaggaccttgtgg--ttgtattgtatcctttgactcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
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gtcaggcactctacttgtatagtttttgctatgatgtgatttgtttttgtggctactgtcttgtttctttgctgaattttttgagaaattgaggggtggcctttgattcaaattgcctgatagtgatgcagGTACGGGCGGGAATCCACTTTTGGGGGAACAAGCTGCAGAGGAATCAAGAGATGCTATTGCTGATGCTCTTAAAGGATCAGATTTGGTGTTTATAACGGCMapped 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|71857956|gb|DT007011.1|DT007011EST: TGCGGCTTCGAACCCTCTCCAAATTGGAGAACTTTTGACTCGTGGACTAG GTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGG
genomic: TGCGGCTTCGAACCCTCTCCAAATTGGAGAACTTTTGACTCGTGGACTAGgtctggcact ... agagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGG
EST:
gi|71865724|gb|DT014779.1|DT014779EST: TGCGGCTTCGAACCCTCTCCAAATTGGAGAACTTTTGACTCGTGGACTAG GTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGG
genomic: TGCGGCTTCGAACCCTCTCCAAATTGGAGAACTTTTGACTCGTGGACTAGgtctggcact ... agagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggaccttgtggttgtattgtatcctttgactcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
acttaat putative branch site (score: 4)
tattgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttttatatgggtggtatagctgcttttgttttcttatgtgttgaggaccttgtggttgtattgtatcctttgactcaaaccacttaatagagatgcagGTACGGGTGGGAATCCACTTTTGGGGGAACAGGCTGCTGAGGAATCAAAGGAAGCCATTGCAAATGCTCTCAAGGGTTCAGATCTTGTGTTTATAACAGC
- - - - -tgggtgg
- - - - - - - - - -agctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacca