Sequence
atgc intronic sequence ATGC exonic sequence...catttgggtatagcgataaaaattttatcctaagaatgcactgttcaggcaaaagttatatcaccgctgttgctaatatttttaaaacatgaattgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g19690.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g19690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G135968_T01 (Zea mays), 3'ss of exon 10
---------------------------------------catttgggtatagcgataaaaattttatcctaagaatgcactgttcaggcaaaagttatatcaccgctgttg--ctaatattt------ttaaaacatgaattgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
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gtaagcttcatttacatggacaggcacctcttcctcctctatctctccatctctagcagaacatggttataaaatcaaactatcatgcctcaaaatttaattctgacaatgatctaaaatttgaccctttttcttaataaccttcagTTTTGTATTATCACTGGCCGGTGTCGATGCTGAACTTCTCATGGAAGAGGAGAGTCTTGTTTGGACAAGTAAAGATGTTGTTATTGTGCTTGAGCATAAC
upper sequence: LOC_Os03g19690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G03880.1 (Glycine max), 3'ss of exon 4
catttgggtatagcgataaaaattttatcctaag--aatg-cactgttcaggcaaaagttatatcaccgctgttgctaatatttttaaaacatgaattg-acagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
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----ttgctgaatgaagaagtattttgatcggtgttgatgatattattttgattcaaaaccaattcaaactgaaatttctaaatgtaatgcttttactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
upper sequence: LOC_Os03g19690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 10
catttgggtatagcgataaaaattttatcctaagaatgcactgttcaggcaaaagttatatcaccgctgttgctaatatttttaaaacatgaa------ttgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
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----ggtgtttatctgcactgctctattatgttgcgtcagctgtgaagtgtatggttttatt--cattaaaatgaatattcaaatgccacaaggtctcttttgcagCTTTGTTCTATCATTGGCTGATGTCGATCCACACCTTATGATGGAAGATGAAAGTCTTGTATGGACAAGTAATGATGTTGTCATTGTGCTTCAGCATCAA
upper sequence: LOC_Os03g19690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0077g00200.t01 (Vitis vinifera), 3'ss of exon 4
catttgggtatagcgataaaaattttatcctaagaatgcactgttcaggcaaaagttatatcaccgctgttgctaatatttttaaaacatgaa------ttgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
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----ggtgtttatctgcactgctctattatgttgcgtcagctgtgaagtgtatggttttatt--cattaaaatgaatattcaaatgccacaaggtctcttttgcagCTTTGTTCTATCATTGGCTGATGTCGATCCACACCTTATGATGGAAGATGAAAGTCTTGTATGGATAAGTAATGATGTTGTCATTGTGCTTCAGCATCAAMapped 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|88387303|gb|CI580648.1|CI580648EST: AAGAAACATGGAGATCTGTACCGGACTTATGGAACCAGAGTGATTCCAGT CTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGA
genomic: AAGAAACATGGAGATCTGTACCGGACTTATGGAACCAGAGTGATTCCAGTgtaaacaact ... gaattgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGA
EST:
gi|29671022|gb|CB667297.1|CB667297EST: AAGAAACATGGAGATCTGTACCGGACTTATGGAACCAGAGTGATTCCAGT CTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGA
genomic: AAGAAACATGGAGATCTGTACCGGACTTATGGAACCAGAGTGATTCCAGTgtaaacaact ... gaattgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggcaaaagttatatcaccgctgttgctaatatttttaaaacatgaattgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
tgctaat putative branch site (score: 2)
taatatttttaaaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttgggtatagcgataaaaattttatcctaagaatgcactgttcaggcaaaagttatatcaccgctgttgctaatatttttaaaacatgaattgacagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG