Sequence
atgc intronic sequence ATGC exonic sequencegtactgtattcctactatgacaatgtggacagattttctggaaaggagtttgatacattatatctggtgttgtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g24220.3 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g24220.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 12
gtactgtattcctactatgac------aatgtggacaga---ttttctggaaaggagtttgatacattatatctggtgttgtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG
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gtactgtattcatattttaaatttttgattatgcataaaatatttcctgtggatgagtttcataacttatttgtggtgttgtagGGTCGTATTTATCAAGGAAAAGAGCCACCACAATTTGTGGCTATTTTCCAGCCAATGGTTATTCTTAAG
upper sequence: LOC_Os03g24220.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 17
gtactgtattcctactatgac------aatgtggacagatttt---ctggaaaggagtttgatacattatatctggtgttgtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG
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gtactgtatttatattttgaatttttgattatgcataaaatatgccctgtggatgagtttcatatcttatttgtgttattgtagGGTCGCATTTATCAAGGAAAAGAACCACCACAATTTGTTGCTCTTTTCCAGCCAATGGTTATTCTTAAG
upper sequence: LOC_Os03g24220.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 12
gtactgtattcctactatgacaatgtggacagattttctggaaaggagtttgatacattatatctggtgtt-gtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG
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-----gtatccgtaatgtgatattatgttggggattttgcttggaaactctgtataattgtaatagtttctcgcagGGTCGCATATTTGATGGTAAAGAGCCACCACAGTTTATTGCCCTTTTCCATCCAATGGTGGTCCTCAAGMapped 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|58670584|gb|CK059270.1|CK059270EST: TCCAAACAGCTAATTCAATTTGGAATTCACTGAAAGGAAGGCCTATTCTG GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAG
genomic: TCCAAACAGCTAATTCAATTTGGAATTCACTGAAAGGAAGGCCTATTCTGgtactgtatt ... ggtgttgtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAG
EST:
gi|88692350|gb|CI735925.1|CI735925EST: NCCAAACAGCTAATTCAATTTGGAATTCACTGAAAGGAAGGCCTATTCTG GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAG
genomic: TCCAAACAGCTAATTCAATTTGGAATTCACTGAAAGGAAGGCCTATTCTGgtactgtatt ... ggtgttgtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgtggacagattttctggaaaggagtttgatacattatatctggtgttgtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG
gtttgat putative branch site (score: 5)
tttgatacattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgtattcctactatgacaatgtggacagattttctggaaaggagtttgatacattatatctggtgttgtagGGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC