Sequence
atgc intronic sequence ATGC exonic sequence...tgttgagaagttatactcaaggaaacattggtagaattgcttatttattgccaagattctaaagatctaatcattgttgtctttcttgtaaatttgccagATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATCAGAATGCTTGGTGAGGTATTCCAGAAGTTAGGGATGTTGGACAAATATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55290.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55290.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G105827_T03 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------------tgttgagaagttatactcaaggaaacattggtagaattgcttatttattgccaa-gattctaaagatctaatcattgttgtctttcttgtaaatttgccagATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATCAGAATGCTTGGTGAGGTATTCCAGAAGTTAGGGATGTTGGACAAATATG
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gtaggaaatggaatttcttttttttcccttatttcaccagtttgcatgctgttttaactaaaagataggatttgacttcataccgtttttttccatgataggaaagctttgctcaaagaaacattagttggggataattatccaagcattcttat-gatgtcttacacctaaattttccagATTTTTGCTGATATGGAGGAACTAGGCGTAAGACCAGATGGTTCTATTATCAGGATGCTAGGTGATGTATTTCAAAAGATAGAGATGATGGACAAATACG
upper sequence: LOC_Os01g55290.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G040970_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------------tgttgagaagttatactcaaggaaacattggtagaattgcttatttattgccaagattctaaagatctaatcat-tgttgtctttcttgtaaatttgccagATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATCAGAATGCTTGGTGAGGTATTCCAGAAGTTAGGGATGTTGGACAAATATG
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gtaggaaatgaaatgtttgttttcttatttcaccagtttgcatgatgttttaactaaaagctggggtttggcttcataccattttccccccatgttagaaaaggctttgctcaacagaaacatcaattgggggataattatccaagcattcttatgatgtcttacacgtaacttctccagATTTTTGCTGATATGGAGGAACTAGGCGTAAGACCTGATGGTTCTATTATCAGGATGCTAGGTGATGTATTTCAGAAGTTAGAGATGATGGACAAATATGMapped 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|163929352|gb|EG713777.1|EG713777EST: GAATGATATCTTTATATTACAGACTAGAATCATATCAGAAGATGTTTGAG ATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATC
genomic: GAATGATATCTTTATATTACAGACTAGAATCATATCAGAAGATGTTTGAGgtaggaatcc ... aatttgccagATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATC
EST:
gi|163919833|gb|EG714403.1|EG714403EST: GAATGATATCTTTATATTACAGACTAGAATCATATCAGAAGATGTTTGAG ATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATC
genomic: GAATGATATCTTTATATTACAGACTAGAATCATATCAGAAGATGTTTGAGgtaggaatcc ... aatttgccagATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgccaagattctaaagatctaatcattgttgtctttcttgtaaatttgccagATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATCAGAATGCTTGGTGAGGTATTCCAGAAGTTAGGGATGTTGGACAAATATG
tttcttgtaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttgagaagttatactcaaggaaacattggtagaattgcttatttattgccaagattctaaagatctaatcattgttgtctttcttgtaaatttgccagATCTTTGCTGATATGGAGGAGCTGGGTGTTAGACCTGACGGTTCGATTATCAGAATGCTTGGTGAGGTATTCCAGAAGTTAGGGATGTTGGACAAATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT