Sequence
atgc intronic sequence ATGC exonic sequence...agatttagaaaattggcttgattcttttttcttatttagtttctaggtaatgggcacttatatatcttgcacataatccttaaattcattcttatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g51430.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------agatttagaaaattggcttgattcttttttcttatttagtttctag-gtaatgggcacttatatatcttgc-acataatccttaaattcattct-tatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
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gtacatctcattcttcaatttttgctttaatataaaattgtcaatgaatatattttccaaataaaatttattttattttct-attaggtatatatcatggtattcacaaatttacattattgcatcaattttgtttttggactatacatcagGGTTGTTGAAATGCAAGAGATCTTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCTGGTGCTATGGCGACAATAACAAACCAACGTAGA
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------------------agatttagaaaattggcttgattcttttttcttatttagtttctaggtaatgggcacttatatatcttgcaca---taatcct----taaattcattctt---atgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
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gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaat--tctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 9
-agatttagaaaattggcttgattcttttttcttatttagtttctaggtaatgggcacttatatatcttgcacataatccttaa--attcattcttatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
| | || | | || | | || ||| || || | || | || | || ||| | || || ||||| || ||||||||||| |||||||| || ||||| ||||| |||| ||||||||||| ||||||||||| | |||||| ||||| | ||||||| | || ||
aacacaaagtctcctatccagaagaaaatgagtagactaatttaaagtgaactagt-taactagaactggtac-taactttcaatggtttattct-atcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 8
agatttagaaaattggcttgattcttttttcttatttagtttctaggtaatgggcactta--tatatcttgcacataatccttaaattcattcttatgt-----tagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
||| | | || | | ||| | ||| | ||| | | || ||| ||||| | || ||| || || | | ||||||||||||||||||||| ||||| ||||||||| |||| || |||||||| ||||||||||| | ||| | ||||| |||| ||||| | ||||||
-------tgcaatagatcactgcatgttattatgtttgaccacatggttcagtttactcaactttagtttgaacatagttttttttttctttgttttctctttgtagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAACTTGCTGAGGAAGCAGCCGAGGCTGAGGGAGGAGGGACCATGGCATCAATTGCAAATCCTCGTAGA
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 8
agatttagaaaattggcttgattcttttttct-tatttagtttctaggt--aatgggcacttatatatcttgcacataatccttaaattcat----tcttatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
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-------gtgcaatagatcactgcatgttattatgtttgaccacatggttcagtttgctcaagtttagtttgaacatggtttttttttctttgttttctctttgtagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAACTTGCTGAGGAAGCAGCCGAGGCTGAGGGAGGAGGGACCATGGCATCAATTGCAAATCCTCGTAGAMapped 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|29666539|gb|CB662814.1|CB662814EST: CCCTCAGACGTTAGTTCGAGCAATAAG GGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGC
genomic: CCCTCAGACGTTAGTTCGAGCAATAAGgtatgcatga ... cttatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtaatgggcacttatatatcttgcacataatccttaaattcattcttatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
ttcattctt CT-rich tract
ttaaattcattcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatttagaaaattggcttgattcttttttcttatttagtttctaggtaatgggcacttatatatcttgcacataatccttaaattcattcttatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
- - - - - - - - - tgattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgca