Sequence
atgc intronic sequence ATGC exonic sequence...tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatttttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g50320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G832989_T01 (Zea mays), 3'ss of exon 5
---------tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatt-tttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
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gtaaatagattcttttgtaccttacaagtctatacaataaattaaataattaaccagtaaagtcatctcgattgaactta---tttgttggttaccttcctggaatgcagGAGGAAAATAAGATCTTGGATAGGCTGCACCGCCAAAAAGTTGCGGAAGTGGAAAAGCTGAGTCAAACTGTGAGAGAGTTGGAAGAGGATGTTCTGCAAG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 5
----------tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatttttcaatttttctcaaactgaattgattatctttctggat-taaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
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gtgctgtactcattatcatcttctttgtatctagttagtcaggctttggatgccttctacttatcactcattgtttgttaa-taatttctattatctgtttgattctttagGAAGAAAACAAAATTCTAGACCGAATGCACAGGCAAAAGGTTGCGGAGGTGGAAAAGCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatttttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
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-------gttctgtg-gtcgccatcttgt--tctttgtatttacttaat-----ctatggatttgccaacaatctgattaactttattttctgtttta-gGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatttttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
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gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattt-tgttttggattttttttgtgtaatc--ttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTGMapped 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|25777864|gb|CA752614.1|CA752614EST: ACATGCAAAACAAGAACCAAGAGTTAATGAAGCAAATTGAGATCTGCCAG GAAGAAAACAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTA
genomic: ACATGCAAAACAAGAACCAAGAGTTAATGAAACAAATTGAGATCTGCCAGgtacatgtct ... tggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatggcatttttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
aattgat putative branch site (score: 4)
ttatctttct CT-rich tract
atttttcaatttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatttttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT