Sequence
atgc intronic sequence ATGC exonic sequence...tgaacttttattttttttattcatataataacacaagttgctgaataattctacgggaaaaaaagcatcgtcctggtcctcacaaatatttttccatcagTTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATTATTTGGAGCCGTCGGGACAATGATATCCTTTTTCACAATATCTATTG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47100.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
tgaactt--ttattttttttattcat-ataataacacaagtt-gctgaataattctacgggaaaaaaagcatcgtcctggtcctcacaaatatttttccatc-----agTTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATTATTTGGAGCCGTCGGGACAATGATATCCTTTTTCACAATATCTATTG
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--aactgaatgatctgttgaatccatgacgccaatcccttctagtttgatacttctttg-------acgtataatcaagattctcacagacgtttcctcacctcaccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 3
tgaacttttattttttttattcatataataacacaagttgctgaataattctacgggaaaaaaagcatcgtcctg-gtcctcacaaa--tatttttcca-----tcagTTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATTATTTGGAGCCGTCGGGACAATGATATCCTTTTTCACAATATCTATTG
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------ttttcaactgggacctgtttaccaagctaggtgactt--tatttaggaaggcaccgtatctctgtccaatgatttcgtaaacctgccgttgcacgtgatcagTTTTCAGGTCAAGAAGAAGCAGTTCTTCCGGAACTTTATTGCCATCATGCTTTACGGAGTAATTGGAGTCTTTATCTCTTTTGCCATTATCTCAGCAGMapped 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|88358188|gb|CI605113.1|CI605113EST: GAGGATCTCTTCTTCATCTACCTCCTCCCTCCGATCATCTTCAATGCAGG TTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATT
genomic: GAGGATCTCTTCTTCATCTACCTCCTCCCTCCGATCATCTTCAATGCAGGgtaagtagaa ... tttccatcagTTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattctacgggaaaaaaagcatcgtcctggtcctcacaaatatttttccatcagTTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATTATTTGGAGCCGTCGGGACAATGATATCCTTTTTCACAATATCTATTG
tcctcac putative branch site (score: 2)
tttttccatc putative PPT
tcacaaatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaacttttattttttttattcatataataacacaagttgctgaataattctacgggaaaaaaagcatcgtcctggtcctcacaaatatttttccatcagTTTTCAGGTAAAGAAAAAGCAATTCTTCCGGAATTTCATGACGATCACATTATTTGGAGCCGTCGGGACAATGATATCCTTTTTCACAATATCTATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG