Sequence
atgc intronic sequence ATGC exonic sequencegtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g02555.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 6
gtgctt--tattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
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gtgattgttgctttgcaatctgtc-tcattttttataat--tttctgcggcattcttttgagttacttatttttt-tat-------tcagTCCCTGCGAAGGATGAACCATCCAAACATTGTAAAGCTCAAAGAAGTCATAAGAGAGAGTGATACGCTGTTCTTTGTTTTTGAGTACATG
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
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gtactgtatctcattagctgaaa--ggttttgtttttttttttttttactgtatgttcgctgatttttttcttttct---cattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 3
gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
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-------gtaaaacagtttatacttctgctc--ttattattgctattttatttc-tgtatatggttttaaatttttt-ctttttgcagTCATTGAGAAAGATGAACCACCCAAACATTGTGAAGCTCAGGGAAGTCTTTAGGGAAAATGATATTTTGTACTTTGTGTTTGAATACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
cattaat putative branch site (score: 3)
atatctattatacttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA