Sequence
atgc intronic sequence ATGC exonic sequence...agatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCAACATGGAAACTAGGGCACCAAGGCCTCTATGCCCCCATTTCCACCTTGCAGCAAGCAAACTGCGAAGATCCTCTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37350.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37350.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G131756_T01 (Zea mays), 3'ss of exon 16
-----agatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCAACATGGAAACTAGGGCACCAAGGCCTCTATGCCCCCATTTCCACCTTGCAGCAAGCAAACTGCGAAGATCCTCTAA-----
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atttcagacacacaa-aggtcatgaacggaagc-agtctctaggtttcaactccacaatgaatttctgaacgaaacaagtaaactgtggctg---tcttacgcagGATTTGTCTGTGTGCGAGGATTCGACATGGAGACTAGAGCACCAAGGCCTCTGTGCCCCCATTTGCACATTATAGCAAGGC-----CGAAGGCCCGCAAGACAGC
upper sequence: LOC_Os05g37350.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G141792_T01 (Zea mays), 3'ss of exon 2
-----agatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCAACATGGAAACTAGGGCACCAAGGCCTCTATGCCCCCATTTCCACCTTGCAGCAAGCAAACTGCGAAGATCCTCTAA-----
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atttcagacacacaa-aggtcatgaacggaagc-agtctctaggtttcaactccacaatgaatttctgaacgaaacaagtaaactgtggcta---ttttacgcagGATTTGTCTGTGTGCGAGGATTCGACATGGAGACTAGAGCACTCAGGCCTCTGTGCCTCCCATTAGCACATATAGCAAGGC-----CGAAGGCCCGCAAGACAGC
upper sequence: LOC_Os05g37350.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G020977_T01 (Zea mays), 3'ss of exon 3
--agatataagtta-gggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCAACATGGAAACTAGGGCACCAAGGCCTCTATGCCCCCATTTCCACCTTGCAGCAAGC---AAACTGCGAAGATCCTCTAA
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acacacaaaggtcatgaacggaagcagtctctactctctagccttcaactccacaatgaatttctgaacgaaacaagtaaactgtggctg---tcttacgcagGAGTTGTCTGTGTGCGAGGATTCGACAGGGAGACTAGGGCACCAAGGCCTCTGTGCCCCCATTTGCACATTGTAGCAAGGCCGAAAGTCCGCAAGACAGC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCAACATGGAAACTAGGGCACCAAGGCCTCTATGCCCCCATTTCCACCTTGCAGCAAGCAAACTGCGAAGATCCTCTAA
cactaaa putative branch site (score: 2)
tcttatactttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCAACATGGAAACTAGGGCACCAAGGCCTCTATGCCCCCATTTCCACCTTGCAGCAAGCAAACTGCGAAGATCCTCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - -cttgttg
- - - - - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - cagctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca