Sequence
atgc intronic sequence ATGC exonic sequence...gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 12
gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctc--ttcatcccatacttgtgatattcaattaca----gGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
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-ctttaattgcttgcaacct--gctagctactgtgt---ttttttgtcatgtccttggcccttgggtttgacttatcttctgttcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
gatatactttttttttacttttgttggccattgcctatctc-tcatg-actcatctctgggcactaacctcttcatcccatacttgtgat-attcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
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-ctttaattgcttgcaacct--gctagctactgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 13
gatatactttttttttacttttgttggccattgcctatctctcatgactcatct-ctgggcactaacct---cttcatcccatacttgtgatattcaattaca----gGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
|||||||| || || | || | | | | | || ||| | | ||| ||||||| | || ||||| ||| ||| |||||| ||||||||||||||||||||||||||||| ||||| || || ||||| ||||||| ||| |||| ||||| || ||||||
--------ttttttttgctattttaatcctataattgcttgcaacctgctagctactgtgtcttccccttgacttcatcttctgctaatgatactcatccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------gatatactttttttttacttttgttggccattgcctat-ctctcatgactcatctctgggcactaacctcttcatcc---catacttgtgatattcaatta----------------cagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
| | |||||| || | | ||| | |||| | | | || | || | | | | | | || ||| | | || | ||| ||||||| ||| | || ||||||||||||||| | ||||||||||| ||||||| |||||||| || |||| || |||| ||||||
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
||| | | | | | | ||| | || |||| | || | |||| | | | | | | |||| | ||||||| ||||| || ||||| || ||||| || |||||||||||| | |||||||||||||| ||| | || || |||||||||||
-gtatgtatatactctccatgtgtcaattttaaaggat------tgacctacctgaagtttctaatggttcttttgctaaaaattcttgttca--tgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
-gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattac--agGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
|| || || | | ||| || ||| | || | | ||| || || | | | || |||| || | || ||||||| ||||| || |||||||| |||||||| ||||| |||||| |||||||||||||||| ||| | || || |||||||||||
gtatgtatttgccacatgatcttgatg--cat-gataatgttttg-aacttatagacattt-ctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------------------------------------------------------------------------------gatatactttttttttacttttgttggccat-tgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
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gtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagggtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatca-tgaagaggaatgttctctattgactgatattatgctcaatt-cagGTTGCTAGTGCATTGGCAGATCCTTACCTTTCATTTGCAGCTGCATTAAATGGTCTAGCTGGCCCACTCCATGGTTTGGCTAACCAGMapped 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|3758954|gb|C96653.1|C96653EST: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST:
gi|38470398|gb|CF954529.1|CF954529EST: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
cactaac putative branch site (score: 1)
atattcaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA