Sequence
atgc intronic sequence ATGC exonic sequencegtgagttatctgatcaatagtttcttctgccttttgttatctttcgctgtttgattatttctactactcttatgcgattgccttactggtggagacagtagtttctttctttatgaatgattatctgttacacatttagcttttcctggttttaattcccgacttttttggatgatggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTGTCTTTTGTACTACTACATCATCTGATACAGAGATATATAAGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g05660.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 5
gtgagttatctgatcaatagtttcttctgccttttgttatctttcgctgtttgattatttctactactcttatgcgattgccttactggtggagacagta-gtttctttctttatgaatgattatctgt-tacacatttagcttttcctggttttaattcccgacttttttggatgatggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTGTCTTTTGTACTACTACATCATCTGATACAGAGATATATAAGCG
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-------------------------------------------------------------------------------------gtgacgaacaacatatatatagtatggtatgtgtgtgtgtgtgcgcgcgcacgca-tgtcaactggatactattgaatactgatg-ggcccgccgtgagcagGAACTGTGAGACGTTTTCTGGAGAAACAAAAGGACAAAATAACAGCTATTGTCTTCTGTACGATATCATCATCTGACACAGAGATATATAAGAG
upper sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G06730.1 (Glycine max), 3'ss of exon 6
gtgagttatctgatcaatagtttcttctgccttttgttatctttcgctgtttgattatttctactactcttatgcgattgccttactggtggagacagtagtttctttctttatgaatgattatctg--ttacacatttagcttttcctggttttaattcccgacttttttggatgatggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTGTCTTTTGTACTACTACATCATCTGATACAGAGATATATAAGCG
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---------------------------------------------------------------------------------------actgttttctgatgtctgatggataatatattattattaggtttctacactttgtattgtccatttgttctatatattcttctaaggtcattttattcagGAACTGTGCGGCGGTTTCTTGAGAAGCAGAAAGACAATATAACAGCTGTTGTCTTTTGCACTACCAGCACAACTGATACTGAGATATATAAAAG
upper sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G12670.1 (Glycine max), 3'ss of exon 6
gtgagttatctgatcaatagtttcttctgccttttgttatctttcgctgtttgattatttctactactcttatgcgattgccttactggtggagacagtagtttctttctttatgaatgattatctg--ttacacatttagcttttcctggttttaattcccgacttttttggatgatggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTGTCTTTTGTACTACTACATCATCTGATACAGAGATATATAAGCG
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---------------------------------------------------------------------------------------gctgttttctgatgtctgatggataatatattattattaggtttctacactttgtattgttcatctgttctatatattcttctaaggtcattttattcagGAACTGTGCGGCGGTTTCTTGAGAAGCAGAAAGACAATATAACAGCTGTTGTCTTTTGCACTACCAGCACAACTGATACTGAGATATATAAAAG
upper sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 5
gtgagttatctgatcaatagtttcttctgccttttgttatctttcgctgtttgattatttctactactcttatgcgattgccttactggtggagacagtagtttctttctttatgaatgattatctgttacacatttagcttttcctggttttaattcccgacttttttggatgatggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTGTCTTTTGTACTACTACATCATCTGATACAGAGATATATAAGCG
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--------------------------------------------------------------------------------atatgtaggttggatatgtagatgagtatgttttgga-agttgagtgttctttatttta-ttctcggatgttcaattcatcgtttatttgttttttgtt---cagGGACAGTGAGGCGGTTTCTTGAGAAGCAGAAGGATAAAATTACTGCTGTTGTCTTCTGTACTACCACAGCAAATGATACTGAGATATATAAAAGMapped 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|33793226|gb|CF322493.1|CF322493EST: TACAGAAGCCAAAAATTACCCTCGTGAACCGGCTGCTCATGTTGCAATAA GAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTG
genomic: TACAGAAGCCAAAAATTACCCTCGTGAACCGGCTGCTCATGTTGCAATAAgtgagttatc ... tggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTG
EST:
gi|58677193|gb|CK065880.1|CK065880EST: TACAGAAGCCAAAAATTACCCTCGTGAACCGGCTGCTCATGTTGCAATAA GAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTG
genomic: TACAGAAGCCAAAAATTACCCTCGTGAACCGGCTGCTCATGTTGCAATAAgtgagttatc ... tggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacatttagcttttcctggttttaattcccgacttttttggatgatggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTGTCTTTTGTACTACTACATCATCTGATACAGAGATATATAAGCG
ttttaat putative branch site (score: 3)
ttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttatctgatcaatagtttcttctgccttttgttatctttcgctgtttgattatttctactactcttatgcgattgccttactggtggagacagtagtttctttctttatgaatgattatctgttacacatttagcttttcctggttttaattcccgacttttttggatgatggtgaacagGAACTGTTAGACGTTTTCTGGAGAAGCAGAAAGGCAAAATAACTGCTGTTGTCTTTTGTACTACTACATCATCTGATACAGAGATATATAAGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT