Sequence
atgc intronic sequence ATGC exonic sequence...tttgtgtttgatttctcaatggcccaaagttgaaaacttaaatctgatgattcatttctggtttatggtatgatatgctgattacttttttgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATGGAAGTCTCCTTGGTTTATGAACTCTTTTCTCCCTGGACCAAGAATTGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 8
tttgtgtttgatttctcaatg--gcccaaagttgaaaacttaaatctgatgattcattt-ctggtttatggta-tgatatgctgattacttttttgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATGGAAGTCTCCTTGGTTTATGAACTCTTTTCTCCCTGGACCAAGAATTGAT
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--ggaattaaacccactactgaagtctgaagagattgttttatgatccttgttccttcagttaatttgtcgttctgaaattctaa--actgttgctcttgttagATTGGCTGATACCCCAGGTATCAAAAGAGGACTAGAATCTCCTTCAGCATGGAAGTCCCCTTGGTTCGTCGATATGCATTTTCAG---------------
upper sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 8
---tttgtgtttgatttctcaatggcccaaagttgaaaacttaaatctgatgattcatttctggtttatggtatgatatgctgattacttttttgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATGGAAGTCTCCTTGGTTTATGAACTCTTTTCTCCCTGGACCAAGAATTGAT
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taaactccgcttg--tctccaactactgaagtgtgaagagattact-tgatccttgttccttttaatatgtaattctgaattctaaagccttgctattgttagATTGGCTGATACCCCAGGCATCAAAAGAGGACTAGAATCTCCTTCAGCATGGAAGTCCCCTTGGTTTGTAGA-TATGCAATTTCAG--------------
upper sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------tttgtgtttgatttctcaatggcccaaagttgaaaactta--aatctga--tgattcat-ttctggtttatggtatgatatgctgattacttttttgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATGGAAGTCTCCTTGGTTTATGAACTCTTTTCTCCCTGGACCAAGAATTGAT
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gtaagataactggtctcactagtgttcctttgtttgaattatctgtttcttttgttagctaatcagttcaggcttcagcgtgtatgaagctaagctgtggcaggttctttttgtcaatatttcttatgaattgctgcttttg---ctagATTGGCTGATACCCCAGGTATCAAAAGAGGACTCGAATCTCCATCTGCATGGAAGTCTCCTTGGTATATCGA----TATGCACATGCACTTTCAG-----
upper sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G08660.1 (Glycine max), 3'ss of exon 11
-----tttgtgtttgat-ttctcaatggcccaaagttgaaaacttaaatctgatgattcatttctggtttatggtatgatatgctgattacttttttgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATGGAAGTCTCCTTGGTTTATGAACTCTTTTCTCCCTGGACCAAGAATTGAT---
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gaactctaatgacaattgttgccattgaccttttgctttaattttcaa----attattcagtgtcaactcactgtg-gttctgacaactgcttgtttgatttc-agATTTGGTGGAACACC---TTTTAGGAAAAGCATTGAATCACCTTCAGCATGGAAATCTCCTTGGTTCATGAACACTTTTTTGTCCAGCCCCAGGATTGATACTMapped 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|30133582|gb|CB918921.1|CB918921EST: ATTCAAAGTTTTAACAT ATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATG
genomic: ATTCAAAGTTTTAACATgtaagttata ... tgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgattcatttctggtttatggtatgatatgctgattacttttttgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATGGAAGTCTCCTTGGTTTATGAACTCTTTTCTCCCTGGACCAAGAATTGAT
tgctgat putative branch site (score: 3)
ttactttttt CT-rich tract
attactttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtgtttgatttctcaatggcccaaagttgaaaacttaaatctgatgattcatttctggtttatggtatgatatgctgattacttttttgggttctagATTTGGTGACACCCCAGGTATTAAAAGAGGAATTGAATCTCCATCAGCATGGAAGTCTCCTTGGTTTATGAACTCTTTTCTCCCTGGACCAAGAATTGAT
- - - - - - - ctcaatg
- - - - - - - - - - - cccaaag
- - - - - - - - - - - - - - -ttgaaaa
- - - - - - - - - - - - - - - - - - - - - -ctgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctg