Sequence
atgc intronic sequence ATGC exonic sequence...tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g59040.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 6
-------tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
| ||| | ||| ||||| | | |||||| | | | | || || | |||||| | | | |||| ||| ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||
gtatttcatgttacagctctatttgtggtagagggaatagaa-------gagctc---tgcttcgacttgtttctaaccttggatttctgttgggcgttg---tcagGGTGAAAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCACTACAACGACATCAGCGAGCTGTCTCCTCACCGCCTGCAAGAGA
upper sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
----tttctactg--ttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
|| || || |||| | | |||||||| | | || |||| ||||| | | || | |||| ||| ||||||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||
gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactc----tgtttcaaactatggctatc-----tgttgggcgttg---tcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
upper sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
-tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
| | | || || | | |||| | ||||| || | | | | || ||| || | | | ||| || | ||||| ||||||||||| || || || |||||||||||||||||||| ||||| || || | |||| ||| || || | ||||| |||||| ||||
gtatattctcttggctctttagctgataaaaaaa---ttgaa-------attttgttccaaccatttaaacaataacaagcttgtccaattgtgaca-cagGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA
upper sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
||||| | ||| | | | || | | | || | | | |||| | | || || | | || | ||| ||||||| || ||||||||||| || ||||| |||| ||||||||||||||| || |||| |||||||| || || |||||||||| ||| || |
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtact-ccaatcttgtatttttggcgctgtaattt-----tagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
upper sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactc---tttttgttttgttt---tttttttactgacgatattggattttg--tgatc---agGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
||| || | | | | ||| || || ||||| | || | || | | | || ||||| ||| ||||||| || ||||||||||| || ||||| |||| |||||||||||| || || || | |||||| ||| || ||||||| || || || |
-----------------gtaacatcctaagctttagtttttcatgtttccttgtgcttcaagtttgtgtaaccattgtagctaattctttggggttttggttgaaataaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
upper sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 4
tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
| | | ||| || | || ||| | || | | | ||||||||| |||||||| || ||||| |||||||| || ||||||||||| || ||| |||| || ||||||| |||| | |||||| | || |||||
-----------------------------------------gtagcaaagtgtttacattcttttcagcgtttctctaagagtgtcatctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCAGAGA
upper sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 5
tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
| | | ||| | | || ||| | || | | | ||||||||| |||||||| || ||||| |||||||| || ||||||||||| || ||| |||| || ||||||| |||| | |||||| | || ||||
-----------------------------------------gtagcaaaatgtttacatccttttcagcgtttttctaagagtgtcatctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCGGAGAMapped 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|33684219|gb|CF312458.1|CF312458EST: GGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCCTGATGCAG GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCCTGATGCAGgtaactccat ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
EST:
gi|33684220|gb|CF312459.1|CF312459EST: GGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCCTGATGCAG GGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
genomic: GGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCCTGATGCAGgtaactccat ... ttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
tactgac putative branch site (score: 1)
tctttttgttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - tactgtt
- - - - - -ctgtttg
- - - - - - - - - -agcaaag
- - - - - - - - - - - - - ggaaaaag
- - - - - - - - - - - - - - - - - acctgca