Sequence
atgc intronic sequence ATGC exonic sequence...tttattagcaagcatttcattctgttgtgagatatttctgttctcttatcatgttgtatatgtatctctaattctcttttttctgatcaaatgaattcagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g25310.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 9
tttattagcaagcatttcattctgttgtgagatatttctgttctcttatcatgttgta----tatgtatctctaattc--tcttttttctgatcaaatgaattcagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
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-----caatgaacacttccattt-ttctgaaaaactgatctctttccagcatgtccaggccttaattatctgaaatatgttcctttttttcgtcaaaccaatgtagCTTGTTTCATGGGAAGAAGGTGGTTACAAGATTTCTGATTATCCGATGCCGAGAGGAGAGGTCGTGGTTGGCGGACACAGTATAACAAAAGGCTATTTCA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 2
tttattagcaagcatttcattctgttgtgagatatttctgttc--tcttatcatgttgtatatgtatctctaattctcttttttctgatcaaatgaattcagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
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tacactggacac--ttccacttccctgaaagactcctcttaccagcatgtccaggccttaattatctgaaatatgttattttttttcgttgaaccaatgtagCTTGTCTCATGGGAAGAAGGTGGTTACAAGATTTCTGATTCTCCAATGCCGAGAGGAGAGGTCGCGGTTGGTGGACACAGTATAACAAAAGGTTATTTCA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 8
tttattagcaagcatttcattctgttgtgagatatttctgttctcttatcatgttgt--atatgtatctctaattctcttttttctgatcaaatgaatt---cagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
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-----------------------gtttgcagacaatct--ttaacacaccatgttgacaatgtgcaagtttattgtaatcatgagtaacaaatttcatcttgcagCTCGTTTCTTGGGAAGAAGGTGGCTACAGAATTTCAGATAAACCAATGCCTAGAGGGGAGATTGTGGTAGGTGGTAACAGTGTAACAGCAGGTTACTTCA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 8
----tttattagcaagca--tttcattctgttgtgagatatttctgttctcttatcatgttgtatatgtatctctaattctcttttttctgatcaaatgaattcagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
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agtttttgtacgcattcaagcacagtagtgtttccagttagaataattcgaggattgagaaccatttttctcaatggacatgtttggtttgac------attgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcatgttgtatatgtatctctaattctcttttttctgatcaaatgaattcagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
ttctgat putative branch site (score: 3)
taattctctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttattagcaagcatttcattctgttgtgagatatttctgttctcttatcatgttgtatatgtatctctaattctcttttttctgatcaaatgaattcagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA