Sequence
atgc intronic sequence ATGC exonic sequence...ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g48090.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 3
------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt--attttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
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aactttagt-caggggaaccaaacacccccttcgtattgtacagtttcctct----tgtacagtttcctctcattttgcacccatt-aaacatattctg--cttatagATAATTAATGCAGTCATGAGTGGAAGAGATGTTCTGGTCATAATGGCAGCTGGTGGAGGGAAGAGTCTATGTTACCAGCTCCCAGCTGTACTTCGTGATG
upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
ggtactgttgagcctagccctagatgtacataccacaacttgctatac-tgcttacagtttctttattttgcatccttttaagcatattgcaaccttc----cagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
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----atcataatcaagggctttagtttatg-atttttttttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG
upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
--------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt-attttgcatccttttaagcatattgcaacct-tccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
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gtaagtgactttctgtattttctgatcctaaatatg-attcttgtgtccgcgtt--tgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
--------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt-attttgcatccttttaagcatattgcaacct-tccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG-----------------------------------------------
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gtaagtgactttctgtattttctgatcctaaatatg-attcttgtgtccgcgtt--tgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
ggtactgttgagcctagccctagat-gtacatacca---caacttgctatactgcttacagt-ttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
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attgttataaaatttatgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaattt-----ttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATGMapped 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|58672003|gb|CK060689.1|CK060689EST: TTTAATGTATTTGGGATTTCTTCATACCGGCAGAATC-AA-AGA-G--AG ATAATCAATGGCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
genomic: TTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAGGTAAGgttagtagaa ... aaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
EST:
gi|58671155|gb|CK059841.1|CK059841EST: TTCATACCGGCAGAATC-AA-AGA-G--AG ATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
genomic: TTCATACCGGCAGAATCAAAGAGAGGTAAGgttagtagaa ... aaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
EST:
gi|29673292|gb|CB669567.1|CB669567EST: TTTAATGTATTTGGGATTTCTTCATACCGGCAGAATC-AA-AGA-G--AG ATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
genomic: TTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAGGTAAGgttagtagaa ... aaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactgcttacagtttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
tgcttac putative branch site (score: 2)
ccttcc putative PPT
agtttctttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA