Sequence
atgc intronic sequence ATGC exonic sequencegtaagagagagggggcttctcactcacccgggcgggatcgaaccccttgcgaatccgccgtcccttccctgaccactagttatgcttgttcgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g37837.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g37837.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G124439_T01 (Zea mays), 3'ss of exon 1
gtaagagagagggggcttctcactcacccgggcgggatcgaaccccttgcgaatccgccgtcccttccctgaccactagttatgcttgttcgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
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-------gtaagtgtccactctcctcgttaccctgcccccatctccttcc----tcacaggctggtctctgactctgaggcgtcctcat--gctgcagGGCAGTTCGAGCTGGATAAGATCCGGCAGGAGCTTAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCC
upper sequence: LOC_Os01g37837.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G014367_T01 (Zea mays), 3'ss of exon 1
gtaagagagagggggcttctcactcacccgggcgggatcgaaccccttgcgaatccgccgtcccttccctgaccactagttatgcttgttcgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
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-----------gtaagtgtccactctcctcgttaccctgcccccgtctccttcctcacaggctggtctctgactctgaggcgtcctcat--gctgcagGGCAGTTCGAGCTGGATAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGACAAGCTCAAAGCT
upper sequence: LOC_Os01g37837.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 1
gtaagagagagggggcttc-tcactc--acccgggcggga-----tcgaaccccttgcgaatccgccgtcccttccctgaccactagttatgcttgtt--cgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
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gtaagtgtccactcccctcattaccctggcccccgcccccctccctcaaacgtcttccagatc--ccggtcggtctctgactctcagtggttcgcgtcgctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC
upper sequence: LOC_Os01g37837.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G355297_T01 (Zea mays), 3'ss of exon 1
gtaagagagagggggcttctcactcacccgggcgggatcgaaccccttgcgaatccgccgtcccttccctgaccactagttatgcttgttcgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT---------
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-------gtaagtgtccactctcctcgttaccctgcccctgtctccttcc----tcacaggctggtctctaactctgaggcgtcctcat--gctgcagGGCAGTTCGAGCTAGATAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCCATACGTACCMapped 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|29633861|gb|CB638870.1|CB638870EST: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA GGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagaga ... ttcgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttgcgaatccgccgtcccttccctgaccactagttatgcttgttcgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
ccctgac putative branch site (score: 3)
cttgttc putative PPT
tagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagagagggggcttctcactcacccgggcgggatcgaaccccttgcgaatccgccgtcccttccctgaccactagttatgcttgttcgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA