Sequence
atgc intronic sequence ATGC exonic sequenceGTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcactttctcctatagttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataaataaaataaatgatgaactctat...
Basic information
species | Oryza sativa |
transcript | LOC_Os07g22720.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 9
GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcactttctcctatagttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataaataaaataaatgatgaactctat---
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GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagtta-ttacttctctggttgagaacagttgatctcttataagttctataagcttatg-catttgtactgctaagttaaatttg-gatgtcttctcgatg
upper sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 5
GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgta---tgtcactttctcctatagttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataaataaaataaatgatgaactctat
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GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGGCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttattacttctctgtttgaaaacatttgttctgtttaagttctaagctatgcatttgtactgtcaagttaaattcg-gatgtttctgccataattg--
upper sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA07G03930.2 (Glycine max), 5'ss of exon 10
GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcactttctc-ctatagttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataaataaaataaatgatgaactctat--------------------------------------------------------------------------
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GTACCTCTCTCTAGCATTAAAGGAACAGGACCTGAAGGGCTCATTGTGAAGGCCGACATTGATGATTACTTGGgtataattctatctttctatatatttgtctgtattctgtacatattttagtggaaacaaatgcttaattgttatgctagagaattcatctgtctatcttgcttgctctaggatatcttgtcatacttggctgattgaattgattatattataacctcttttgccatctgatgcag
upper sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 5'ss of exon 10
GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcactttctcctatagttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataa-ataaaataaatgatgaactctat--
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GTTCCTCTTCAAAGCATCAAAGGGACGGGTCCTGATGGACGCATTGTGAAGGCTGATATTGAAGATTATTTGGgtatgcttttctcta-tgtgcttttgcagattatcctgttacttgcttgattaa--tttagctagataatcaacaattatggagacaatgctgtcttaagtac
upper sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 11
GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcactttctcctata--gttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataaataaaataaatgatgaactctat
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GTACCTCTTTCAAGCATCAAAGGAACGGGTACTGGTGGAAGCATTGTGAAGGCTGATATTGAAGATTACTTGGgtatattttatttttatacactattcttcaatggtaatttaagctgattattggaaattttatttatattttccacta--taatgtag--------------Mapped 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|58680453|gb|CK069140.1|CK069140EST: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGG CTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCAGGGCTAAGTTACACCG
genomic: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcact ... acttctgtagCTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCAGGGCTAAGTTACACCG
EST:
gi|58652754|gb|CK041434.1|CK041434EST: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGACGATTACTTGG CTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCAGCGCTAAGTTACACCG
genomic: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcact ... acttctgtagCTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCAGGGCTAAGTTACACCG
EST:
gi|55410697|gb|CV723073.1|CV723073EST: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGG CTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCAGGGCTAAGTTACACCG
genomic: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcact ... acttctgtagCTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCAGGGCTAAGTTACACCG
EST:
gi|58665439|gb|CK054125.1|CK054125EST: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGG CTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCA
genomic: AACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcact ... acttctgtagCTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
71 (upstream exon),
56 (downstream exon)
Score:
31GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcact ... acttctgtagCTAAGGGTTGCAGAAAGGAAGCTCTTGCGGCTCCAGGGCTAAGTTACACCGATGTTCCCAATGCACAAATAAGAAAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcactttctcctatagttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataaataaaataaatgatgaactctat
- - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa