Sequence
atgc intronic sequence ATGC exonic sequence...catctctgcatccggctgtcctctaagattgatgcaaacaaaagaacaacaaaaatccttgaatattaagctcacaaggttttcccctgttcctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAAGAACTATTGGAACACCCACCTGAAAAAGAGGTTGGCCAAGATGGGAATT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g33660.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g33660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G079123_T01 (Zea mays), 3'ss of exon 1
catctctgcatccggctgtcc--tctaagattgatgcaaacaaa--agaacaacaaaaatccttgaatattaagctcacaaggttttcccctgtt-cctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAAGAACTATTGGAACACCCACCTGAAAAAGAGGTTGGCCAAGATGGGAATT
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---ctcttagttctgtactccaacctagaatttcggcatacatggtagatgaatacaagatgtt-aattttaaa-tcataggttcgtttcatggcacttgttcagGTGGTCGGCCATTGCAACCCATCTACCAAATCGCACGGACAATGAGATCAAGAACTACTGGAACACACACCTCAAGAAAAGGCTGGCCAAGATGGGGATC
upper sequence: LOC_Os08g33660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G111117_T01 (Zea mays), 3'ss of exon 2
catctctgcatccggctgtcctctaagattgatg-caaacaaaagaacaacaaaaatccttgaatattaagctcacaaggttttcccctgttcctgtt-cagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAAGAACTATTGGAACACCCACCTGAAAAAGAGGTTGGCCAAGATGGGAATT
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-cttccttcacaacgtagaatttcggcacacatggtatattggtagatgaaaacaagatgttaatttcaaagt-atacctttgtttcatggtactgtttcagGTGGTCGGCCATTGCAACACATCTACCAAATCGCACGGACAACGAGATCAAGAACCACTGGAACACGCACCTCAAGAAAAGGCTGGCCAAGATTGGGATC
upper sequence: LOC_Os08g33660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0000g06410.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------catctctgcatccggctgtcctctaagat-tgatgcaaacaaaagaacaacaaaaatccttgaatattaagctca--caaggttttcccctgttcctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAAGAACTATTGGAACACCCACCTGAAAAAGAGGTTGGCCAAGATGGGAATT
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gttaactaaactagatcttatgaatcttcaaatgccctgcacatgatacaaaagttgggcattttttaagtctttttgaaat-gattaaattttggaatatggttttgtaggacatgcttcacagggttgtaaattgtgggtggaattgtaatttgggtattgttttatgcagGTGGTCAGCTATAGCAACCCACTTACCAAATAGAACAGACAATGAGATCAAGAATTATTGGAACACACATCTCAAGAAAAGGTTGGCCAAGATGGGAATA
upper sequence: LOC_Os08g33660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
catctctgcatccggctgtcctctaagattg-atgcaaacaaaagaacaacaaaaatccttgaatattaagctcacaaggttttcccctgttcctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAAGAACTATTGGAACACCCACCTGAAAAAGAGGTTGGCCAAGATGGGAATT
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-tttgttttgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgcgtggagcacagaaaaattgattttttggaatgtgttgttgttgattcgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATTMapped 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|66923102|gb|CX109950.1|CX109950EST: AGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAG GTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAA
genomic: AGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAGgtaacaatga ... tcctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaacaaaaatccttgaatattaagctcacaaggttttcccctgttcctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAAGAACTATTGGAACACCCACCTGAAAAAGAGGTTGGCCAAGATGGGAATT
agctcac putative branch site (score: 3)
ttttcccctgttcctg putative PPT
ttgaatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catctctgcatccggctgtcctctaagattgatgcaaacaaaagaacaacaaaaatccttgaatattaagctcacaaggttttcccctgttcctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAAGAACTATTGGAACACCCACCTGAAAAAGAGGTTGGCCAAGATGGGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - tgcatcc
- - - - - - - - - - - - - - -tgatgca
- - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - caacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgaat