Sequence
atgc intronic sequence ATGC exonic sequence...ttatctaatttgattgaaagaacttatgatgttaagtttgcatgtgcgttcagggagaggctagctcactctttgtttttttttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04254.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g04254.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G021849_T02 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------ttatctaatttgattgaaagaacttatgatgttaagt-------ttgcatgtgcgttcagggagag-gctagctcactctttgtt----tttttttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
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gtaagccattccttgaaacgtctctcttttagcatattatctgacctttacaatgtgtgcgtgcgtgcgcacctgcgtggagagagagtggctacaagtttacatgaaatacttatgggtgaatttatgctgcttgttaagacagttgtgcttacactttcattttttctgcctccatagGTGCATCATGGTGGCGCTGGAACAACAGCCGCAGGTCTCAAAGCAGCG
upper sequence: LOC_Os04g04254.2 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ09619 (Selaginella moellendorffii), 3'ss of exon 10
ttatctaatttgattgaaagaacttatgatgttaagtttgcatgtgcgttcagggagaggctagctcactctttgttt--ttttttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
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---------------------------------------gtacgt-ttctcatgacaactttcttttgcaattcatccaaccctctctttctatgtc-gtagGTTCATCATGGAGGCGCGGGAACAACAGCTGCCGGTCTCAAAGCTGCG
upper sequence: LOC_Os04g04254.2 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ38334 (Selaginella moellendorffii), 3'ss of exon 9
ttatctaatttgattgaaagaacttatgatgttaagtttgcatgtgcgttcagggagaggctagctcactctttgtttttttttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
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----------gtacaaagtttatttcttctcctcgattcgcg-attcgcttgagttgagttcttttaaaactggatgctggacttttgttcc------agGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
upper sequence: LOC_Os04g04254.2 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ18041 (Selaginella moellendorffii), 3'ss of exon 10
ttatctaatttgattgaaagaacttatgatgttaagtttgcatgtgcgttcagggagaggctagctcactctttgtttttttttttttttacttct-gtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
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---------------------------------------gtatgtttgt-catgacaactttcttttgcaattcatccaaccctctctttatatgtcgtagGTTCATCATGGAGGCGCGGGAACAACAGCTGCCGGTCTCAAAGCTGCGMapped 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|218504178|gb|FG958866.1|FG958866EST: TACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTG GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
genomic: TACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTGgtaagcattt ... acttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgttcagggagaggctagctcactctttgtttttttttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
agctcac putative branch site (score: 3)
ctagctcactctttgt CT-rich tract
tttgtttttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatctaatttgattgaaagaacttatgatgttaagtttgcatgtgcgttcagggagaggctagctcactctttgtttttttttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - -ttgattg
- - - - - - - - aaagaac
- - - - - - - - - - - - -atgatgt
- - - - - - - - - - - - - - - - - - - tgcatgt