Sequence
atgc intronic sequence ATGC exonic sequencegtatctatctttatactttttaaagttgtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g50320.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G832989_T01 (Zea mays), 3'ss of exon 3
----gtatctatctttatactttttaaagttgtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
||| |||| | ||| | ||||| ||||||||| | || |||||| |||| | |||||||||| |||||||| |||||||||||||||||||||||||| |||||||||||||||||||| || |||||||| || |||||||| |||| ||| || ||||
gtatgtacatatcctatgactcccttttgttgtctctgccccctcaat--tggttgctctttgatcactagagttttgcagAACCTAGAACTGAAGAAAACAAATGATGAGAAAAAGGCTGCTATGGCTGCTCAGTTTGCGGCGGAAGCAACACTACGAAGAGTACATGGAGCTCAGAAAG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
---------gtatctatctttatactttttaaagtt---gtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
| | | | | ||| | | |||||| | | || | | | | | | ||||||||||| ||| | ||||||| |||||||| || || || | ||||| |||||||||||||| ||||| ||||| ||||| || ||||| || || || |
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gtatctatctttatactttttaaagttgtttctgcccccctcttt---ttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
|||||| || | | |||| | | || | || | |||| | | | |||||||||||||| ||||||||| ||||| || || || || | ||||||||||||||||| || ||||| ||| | ||||||| ||||| || ||||| |
gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatctatctttatactttttaaagttg---tttctgcccccctctttttgattgctccctgatggagaac-attttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
|| | | ||| | | | | | | ||| | | | | ||||| |||| || ||||||||||||||| ||||||| | ||||| ||||| ||||| | ||||||||||||||||| || ||||| || | |||| || ||||| || ||||| |
------------gtatgtatcaaaatctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
----------gtatctatctttatactttttaaagttgtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
| | || | | ||| ||||| | | || | ||| || ||| | | ||||||||||||| || ||||||||| |||||||| || ||||| | ||||||||||| |||||||||||||| ||||| |||| || ||||| || || || |
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgt-tttgcagttttgtcctaaca-attgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
upper sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------gtatctatc-tttatactttttaaagttgttt-ctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
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gattctcgcattttttgtcttatgtggacgtcgtttctttgtgctaaaattttaagttgtttctttgttacttatcagtatttg--gggggtgtttttgcagAACCTTGAATTGAAGAAGCTCAATGACGAGAAGAAAGCAGCTCTGGCCGCCCAGTTTGCAGCGGAGGCAACTCTGCGAAGGGTGCATGCAGCTCAGAAAGMapped 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|29636308|gb|CB641317.1|CB641317EST: AGAAGCTGGATGAGAAACTCAAGCTAACAGAGTCTCTCCTTGAAAGCAAA AATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCT
genomic: AGAAGCTGGATGAGAAACTCAAGCTAACAGAGTCTCTCCTTGAAAGCAAAgtatctatct ... cattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttgtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
ccctgat putative branch site (score: 4)
tttttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctatctttatactttttaaagttgtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA