Sequence
atgc intronic sequence ATGC exonic sequence...tcttactgttctctattctgggggaggggattggggccatgtaacttcggtgtccccacaatgatttgtcctcctaatgtggttttaccatttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g47240.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 2
tcttactgttctctattctgggggaggggattggggccatgtaacttcggtgtccccacaa---tgatttgtcc-tcctaatgtggttttaccatttatatca------gTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG
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-------atccactttccatttgagcaattttcaaatcatg---cttaagtttccgcaaacctttgctttgtataccctatcttgataccatcatctgtattactattagTGATAGTGGTGAAATGTGCGCAATGAAAGAGGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAGAGTGCAAAGCAATTGGGGCAG
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
---tcttactgttctctattctgggggaggggattggggccatgtaacttcggtgtccccacaatgatttgtcctcctaatgtggttttaccatttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG
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ataaactgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccc--tgttttgat-cggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
tcttactgt-tctctattctgggggaggggattggggccatgtaacttcggtgtccccacaatgatttgtcctcctaatgtggttttaccatttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG
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-cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAAMapped 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|4715352|gb|AU056469.1|AU056469EST: AAGCTAATTGGCCGTGGAACATTTGGTCATGTATATGTTGGCTTTAACAG TGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGA
genomic: AAGCTAATTGGCCGTGGAACATTTGGTCATGTATATGTTGGCTTTAACAGgtaagaatat ... tttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGA
EST:
gi|58598471|gb|CK008999.1|CK008999EST: AAGCTAATTGGCCGTGGAACATTTGGTCATGTATATGTTGGCTTTAACAG TGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGA
genomic: AAGCTAATTGGCCGTGGAACATTTGGTCATGTATATGTTGGCTTTAACAGgtaagaatat ... tttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcggtgtccccacaatgatttgtcctcctaatgtggttttaccatttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG
tcctaat putative branch site (score: 2)
ttttaccatttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttactgttctctattctgggggaggggattggggccatgtaacttcggtgtccccacaatgatttgtcctcctaatgtggttttaccatttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG