Sequence
atgc intronic sequence ATGC exonic sequenceATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagctgcaaacaatacatctttatttatcttcagctaccaagtgcatatattcatgaaacatcctttttttctag
Basic information
species | Oryza sativa |
transcript | LOC_Os11g36470.1 |
intron # | 20 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G418232_T01 (Zea mays), 5'ss of exon 3
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgtta--ttagctgcaaacaatacatctttatttatcttcagctaccaagtgcatatattcatgaaacatcctttttttctag
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GTCTGACATCTTGTATTATGAAGTGTTGGATATACCACTGCCAGAATTGCAGTTCCTAAAAACCCTGAAAGTTGCATTTCACCATCCTACGAAGGATGAGgtttgttttgctaccagacacatatggtgtactgcctatag-tattgtgtgtatatcttcatatgatatccttcct--ccag
upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 20
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagctgcaaacaatacatc---tttatttatcttcagctacca--agtgcatatattcatgaaaca-tcctttttttctag
|| || || | || ||||| || |||||||| || |||||||||||||| |||| ||||| || ||| || | ||||| |||||||| |||||||| || | || || || | ||| | | | | | ||| |||| |||| | | | | | | || | ||
TTCTGATATTCTATACTATGAAGTATTGGATATCCCTCTGCCAGAATTGCAATGCCTAAAAACTCTTAAAATTACTTTCCATCATGCTACCAAGGATGAAgtaagctttgtcagtcaccactttcaatttttacacaataaatttccatcagtgt-tatacttctaaccgagttatccttgttcag
upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 24
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagctgcaaacaatacatctttatttatcttcagctaccaagtgcatatattcatgaaacatcctttttttctag-----
|| || |||||||| ||||| || | || || || ||||||||||| || || ||||||| |||||||||||||| |||||||| || |||||||| || | || | | ||| ||| ||| || || | | || | | | ||| || | || ||| |
TTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATGAAgtgagtatat---agtaatctgattttcttttggttt--ttatctggattatct-tccgtgacacttttttatttgtttattcag
upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 24
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagctgcaaacaatacatctttatttatcttcagctaccaagtgcatatattcatgaaacatcctttttttctag-----
|| || |||||||| ||||| || | || || || ||||||||| | || || ||||||| |||||||||||||| ||||||||||| |||||||| || | || | | ||| ||| ||| | | || | || | || | | ||| | | | || ||| |
TTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAACTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCTACCAAGGATGAAgtgagtatat---agtaatctgattttgttt-tggttttttatctagagtattt-tccataacagttttttatttgtttattcag
upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 20
lower sequence: AT3G11910.1 (Arabidopsis thaliana), 5'ss of exon 24
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagctgcaaacaatacatctttatttatc-ttcagctaccaagtgcatatattcatgaaacatcctttttttctag-------
|| ||||||||||||||||| || ||||||||||| || ||||||||||| || || || || || ||||| || ||||| ||| ||||||||||| || || | |||| | | ||| | || || || || | | | | | | | | | |
GTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATGAAgt-atggattttaaacttaaatttgcgattcgtagctctcttatcacatgttattgtctttaaggcttaataaatcttaaatatacag
upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 24
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagctgcaaacaatacatctttatttatcttcagctaccaagtg-catatattcatgaaacatcctttttttctag---------------------
|| || || || |||||||| || | || || || || ||||||||||| || ||||||| ||||||||||| || || ||||||||||||||||| || | | || ||| || || || ||| | | | | | ||| || | | | | || | |
TTCTGATATTTTATATTATGAAGTTCTAGACATCCCTCTTCCAGAATTGCAAGGTCTGAAAAATCTGAAAGTTGCTTTTCATCATGCTACAAAGGATGATgtgagttaatg--aactatctattttccaccatcgtacctttctatatatcattgatgttttttttaagcctattgtgcaatctcatttggactattttcag
upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 24
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgt---tattagctg---caaaca----atacatctttatttat-cttcagctaccaagt---gcatatattcatgaaacatcctttttttctag-------
|| || ||| | |||||||| || ||||| || || ||||||||| | || || || ||||| |||||||||| || ||||||||||||||||| || || || | ||| || ||| | |||||| | ||| | | || || | | |||| | | || | ||| | |
TTCTGATATACTATATTATGAAGTATTGGACATCCCTCTGCCAGAACTACAAGGTCTTAAAACTTTGAAAGTTGCCTTTCACCATGCTACAAAGGAAGAAgtgcgtacagaccatgacaatcatcttatattttcttatttgttctttatatgtcatgtcaagtttttatttttagtaattcttgatttaattgttctcagMapped 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|58665067|gb|CK053753.1|CK053753EST: AGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAG GTTGTGATTCACAGTATCAGGCTTCCAAAGAATAGCACCATTGCAGACGTG
genomic: AGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagct ... ttttttctagGTTGTGATTCACAGTATCAGGCTTCCAAAGAATAGCACCATTGCAGACGTG
EST:
gi|58674845|gb|CK063532.1|CK063532EST: AGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAG GTTGTGATTCACAGTATCAGGCTTCCAAAGAATAGCACCATTGCAGACGTG
genomic: AGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagct ... ttttttctagGTTGTGATTCACAGTATCAGGCTTCCAAAGAATAGCACCATTGCAGACGTG
EST:
gi|58661692|gb|CK050372.1|CK050372EST: GGCCTGGAAAACC-TGAAAGTTGCATTCCNAC-ATGCTACAAAGGATGAG GTTGTGATTCACAGTATCAGGCTTCCAAAGAA
genomic: GGCCTG-AAAACCCTGAAAGTTGCATTCC-ACCATGCTACAAAGGATGAGgttattagct ... ttttttctagGTTGTGATTCACAGTATCAGGCTTCCAAAGAA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
75 (upstream exon),
46 (downstream exon)
Score:
20ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagct ... ttttttctagGTTGTGATTCACAGTATCAGGCTTCCAAAGAATAGCACCATTGCAGACGTGATTAATGATTTGAAAACAAAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATGAGgttattagctgcaaacaatacatctttatttatcttcagctaccaagtgcatatattcatgaaacatcctttttttctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG