Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctactatcttgttcttatttctcctgctcctttgcccccaaggatatggctactactgcttgatgtcctgttgcttagagtgttcttggctggttgctttcagTTCTTGATTGGTTCATACCTTGGTGCCAAGAAATGGAGGTGGAGGCGATGGAGAAGAAGGGACACAGAGCCTTTGCTAAGGCAATTAAGTCTTTCGGTTC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g55890.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g55890.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G843914_T02 (Zea mays), 3'ss of exon 1
gtaagttctactatcttgttcttatttctcctgctcctttgcccccaaggatatggctactactgcttgatgtcctgttgcttagagtgttcttggctggttgctttcagTTCTTGATTGGTTCATACCTTGGTGCCAAGAAATGGAGGTGGAGGCGATGGAGAAGAAGGGACACAGAGCCTTTGCTAAGGCAATTAAGTCTTTCGGTTC--
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gtgagcccttgtttctcttcttcgtctccgtcgctg-tttgctcg-------gtgtct--tactggcttagactcgtttgcatatttttttttaaa--------tttcagTTCTTGATTGACTCTTAGCTC--TGCCGCGGCATGGAGGTGGAGGCTCTGGAGAAGAAGGGGCACGCAGCTTTTGCCAAGGCGATGAAATCTTTCGGCTCTT
upper sequence: LOC_Os03g55890.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G843914_T01 (Zea mays), 3'ss of exon 1
gtaagttctactatcttgttcttatttctcctgctcctttgcccccaaggatatggctactactgcttgatgtcctgttgcttagagtgttcttggctggttgctttcagTTCTTGATTGGTTCATACCTTGGTGCCAAGAAATGGAGGTGGAGGCGATGGAGAAGAAGGGACACAGAGCCTTTGCTAAGGCAATTAAGTCTTTCGGTTC--------------------
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gtgagcccttgtttctcttcttcgtctccgtcgctg-tttgctcg-------gtgtct--tactggcttagactcgtttgcatatttttttttaaa--------tttcagttcttgattgactcttagCTC--TGCCGCGGCATGGAGGTGGAGGCTCTGGAGAAGAAGGGGCACGCAGCTTTTGCCAAGGCGATGAAATCTTTCGGCTCTTCCGAGCGGTACAAGCGATMapped 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|41884183|gb|BX929014.1|BX929014EST: TCTCTTCTCTTTCCTGCTTCCGAGTTCTGTGAGCCAGCCAACTAATCTCT TTCTTGATTGGTTCATACCTTGGTGCCAAGAAATGGAGGTGGAGGCGATGG
genomic: TCTCTTCTCTTTCCTGCTTCCGAGTTCTGTGAACCAGCCAACTAATCTCTgtaagttcta ... ttgctttcagTTCTTGATTGGTTCATACCTTGGTGCCAAGAAATGGAGGTGGAGGCGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctactactgcttgatgtcctgttgcttagagtgttcttggctggttgctttcagTTCTTGATTGGTTCATACCTTGGTGCCAAGAAATGGAGGTGGAGGCGATGGAGAAGAAGGGACACAGAGCCTTTGCTAAGGCAATTAAGTCTTTCGGTTC
gcttgat putative branch site (score: 5)
ttgctttc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctactatcttgttcttatttctcctgctcctttgcccccaaggatatggctactactgcttgatgtcctgttgcttagagtgttcttggctggttgctttcagTTCTTGATTGGTTCATACCTTGGTGCCAAGAAATGGAGGTGGAGGCGATGGAGAAGAAGGGACACAGAGCCTTTGCTAAGGCAATTAAGTCTTTCGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG