Sequence
atgc intronic sequence ATGC exonic sequence...tgtatgaggtaagacttgggtttttaccccttctattctgtttataatgcctatccagaatttataaatctgtgtaatcctttgtaccctttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g37832.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G090647_T05 (Zea mays), 3'ss of exon 3
tgtatgaggtaagacttgggtttttaccccttctattct-gtttataatgcctatccagaatttat-aaatctgtgtaatcctttgtaccctttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC
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--tttggtttcagagctaagaaataccttcccctatttttgtctatagttctcatccaaaaaatgttaaatatgtgtaatcctgtcttcctgttggttgtagGTTCACATCAGATGTTAAGATCAAGAGCATTTCTGTTGTTGGTGGTGCTGATGGAACAAGCCCGTCAAGAATGAGAGC
upper sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G29400.1 (Glycine max), 3'ss of exon 3
tgtatgaggtaa-gacttgggtttttaccccttctatt--ctgtttataatgcctatccagaatttataaatctgtgtaatcctttgtaccctttggtt----gtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC
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-caacaagccaacgactttatctgtaacatcttccattttctatttagaaaactggtcc------tataagttcttaccgaacttgttatgcttctgtgcaaaatagATTTACTTCAGATGTCAAGATTAAGAGCATATCCATAGTTGGTGGAGCTGATGGAACAAGTCCTTCCAAGATGAGAGT
upper sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G25950.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------tgtatgaggtaagacttgggtttttaccc---------cttctatt--ctgtttataatgcctatccagaatttataaatctgtgtaatccttt----gtaccctttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC
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gtatgtctgttatttgcttaattaccgaccagttacttcaattttcttctaatattattggtttggatatatgaatatagtgtatttcagatcattgacttgaaagaagcttgggagaactagatacagtccatgttttcttactattaaattgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT
upper sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g00760.t01 (Vitis vinifera), 3'ss of exon 3
tgtatgaggtaagacttgggtttttaccccttctattctgtttataatgcctatccagaatttataaa----tctgtgtaatcctttgtaccctttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC
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--taatttgttggtgttactatctttttatttttattgtttttttttttccta--gaggggtgaaaaagtgttctgatttatttgctggaattaattgtgatagGTTTACATCAGATGTTAAGATCAAAAGTATTTCAGTTGTTGGTGGTGCTGATGGAACAAGTCCTTGCAAGATGAGAGCMapped 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|58678373|gb|CK067060.1|CK067060EST: GAGGGTGACCCTGAGTTACTTGTTTTCATCCC GTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGA
genomic: GAGGGTGACCCTGAGTTACTTGTTTTCATCCCgtaagtatgc ... ttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgcctatccagaatttataaatctgtgtaatcctttgtaccctttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC
tcctttgtacccttt CT-rich tract
agaatttataaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtatgaggtaagacttgggtttttaccccttctattctgtttataatgcctatccagaatttataaatctgtgtaatcctttgtaccctttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA