Sequence
atgc intronic sequence ATGC exonic sequencegtgagcactcttctgaatgtatgatgtgttttatagtttgcaccgttaacgactcttttctctacacttccacagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAGGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g05050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g05050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------gtgagcactct-tctgaatgtatgatgtgttttatagtttgcaccgttaacgactcttttctctacacttcc---acagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAGGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGC
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gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
upper sequence: LOC_Os07g05050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------------------------gtgagcactcttctgaatgtatgatgtgtt-ttatagtttgcaccgttaacgactcttttctct--acac----------ttccacagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAGGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGC
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gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTCMapped 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|29670146|gb|CB666421.1|CB666421EST: TTGCCTCTGAGCACTATGGGAAGCCATCAATTCTTGGTCCATTGATCAAA GAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAG
genomic: TTGCCTCTGAGCACTATGGGAAGCCATCAATTCTTGGTCCATTGATCAAAgtgagcactc ... acttccacagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAG
EST:
gi|58599125|gb|CK009653.1|CK009653EST: CAATTCTTGGTCCATTGATCAAA GAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAG
genomic: CAATTCTTGGTCCATTGATCAAAgtgagcactc ... acttccacagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgatgtgttttatagtttgcaccgttaacgactcttttctctacacttccacagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAGGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGC
cgttaac putative branch site (score: 3)
ctcttttctctacact putative PPT
ttttatagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcactcttctgaatgtatgatgtgttttatagtttgcaccgttaacgactcttttctctacacttccacagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAGGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT