Sequence
atgc intronic sequence ATGC exonic sequencegtaatggcgatgaaatcatttttttctctattatctctgtaggaatggtgcaacgtaacaacaagaaacagtgaagttgctgttcattttatcccagcttcttccctcggcgcttaattcactcacttgtcctcatggcagATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02170.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G092776_T03 (Zea mays), 3'ss of exon 14
gtaatggcgatgaaatcatttttttctctattatctctgtaggaatggtgcaacgtaacaacaagaaacagtgaagttgctgttcattttatcccagcttcttccctcggcgcttaattcactcacttgtcctcatggcagATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAG
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------gtacaacaataacttatcccttctccacttaaaatgcagagatacca-gtaatctccagctaca---aatatgtcctgtgttttttacctgctcatatct------cttaactagc---ctctgcttcactgcagATGGTTGCAGGGAGATTTGTGAATGTGTACTCGAGAGATGACTGGATTCTCGGTGTAACCTTCCGAGCAAG
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 12
gtaatggcgatgaaatcatttttttctctattatctctgtaggaatggtgca-acgtaacaacaagaaacagtgaagttgctgttcattttatcccagcttcttccctcggcgcttaattcactcacttgtcctcatggcagATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAG
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---gtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttc--atgaagtagtcccactatcttctatgcagcctta--tcacctcctgctatt--ttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTTGGGGTTGCCTTTCGTGCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatcccagcttcttccctcggcgcttaattcactcacttgtcctcatggcagATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAG
cactcac putative branch site (score: 2)
cttgtcctc CT-rich tract
ttaattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggcgatgaaatcatttttttctctattatctctgtaggaatggtgcaacgtaacaacaagaaacagtgaagttgctgttcattttatcccagcttcttccctcggcgcttaattcactcacttgtcctcatggcagATGGTTGCTGGAAGATTTGTGAATGTGTACTCCACAGATGACTGGATTCTTGGTGTTACTTTTCGTGCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG