Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g51460.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G166889_T01 (Zea mays), 3'ss of exon 11
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
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-----------------------------gtaagttttat--acgcttcaatct--gatgaacaatgatcagaacttcgttcattagcgaatgtataat-----agaataagttgctgttgttggc---cgccgcgcgcagCTCTGCTGTGCAAGATTGGGGCCTTGAGATCGTTCTCGCTGGAGAAGATACACTACTGGAGGGAGAGAGCGTCCGGCATGAGCTCGCTGGCATACTTCCT
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G06550.1 (Glycine max), 3'ss of exon 10
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
| | |||| || | || | || || |||||| || | |||| | | | ||| | | | ||| | | | | || |||||||| | || |||||||||| ||| || ||| |||| |||||||| || |||| |||||||||||||| ||||| ||||| ||| |||| | ||| |
------------------cttataaagaagacaaaatt-ttgatttgtttttttcactaaattttcatttaagctaagctttatgtgtgtcttccc-----------------tcatacgtattgcacat-----ttgcagCTTTACTTTGCAAGATTGCAGCACTCAGAGCATTTTCTCTGGATAAATTACAATACTGGAGGGAGAGTGCATCAGGAATTAGCAGTCTGGCTCATTTCTT
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G20750.1 (Glycine max), 3'ss of exon 10
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagt-aagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
||| | | || | | || ||| | | || |||| | ||||| ||| ||| || | | | | | |||||||| | || |||||||||| ||| || ||| |||| |||||||| || |||| |||||||||||||| ||||||||||| || |||| | || |
---------------------------------------tccttagaaagaagacaaaattttgat-tttttttcccac-taatttttcattaagttaagctgtataagtttcttccctcattcatattgcac-atttgcagCTTTACTTTGCAAGATTGCAGCACTCAGAGCATTTTCTCTGGATAAATTACAATACTGGAGGGAGAGTGCATCTGGAATTAGTAGTCTGGCTCATTTTTT
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G35310.1 (Glycine max), 3'ss of exon 13
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
| | | | | | | | ||| | || || | || || | | || || | | || | || | |||||| ||||||| |||||||| || | || |||||||||| |||||||| || ||||||| ||||||||||| | ||||| |||||| ||||| || ||| |
------------------------------------------gtaagtcacataaatatcactaa--ataatgtaccaactacctagcattcatgtgagcaatgctttattcttatctattgt------tgttaatttcagCTCTTCTGTGCAAAATAGCGGCCTTGAGATCATTTTCTCTGGATAAATTACACTATTGGAGGGAGAGTGATTCTGGCATGAGCAGCTTGGCTTATTTCCT
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G32210.1 (Glycine max), 3'ss of exon 12
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
|||| | | || | || ||| ||| ||||| || || ||| || | | || || | | | | || || | |||||| ||||||| |||||||| || | || |||||||||| |||||||| || ||||||||||||||||||| | ||||| |||||| ||||| || ||| |
-------------------------gtaagtcatataaatataaatatcatt-------aaacaatgt--atctactacctagcattcatgtgagcaatgctttattcttatctattat----------tgttaatttcagCTCTTCTGTGCAAAATAGCGGCCTTGAGATCATTTTCTCTGGATAAATTACACTACTGGAGGGAGAGTGATTCTGGCATGAGCAGCTTGGCTTATTTCCT
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv13s0019g04600.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
|| | || ||| | ||| | | || | |||||| || | || | | || | | | || | | | ||| ||| ||||||| || || || |||| || |||||||||| |||||||||||| |||| |||||||| ||||| |||||||| || ||| |||| || || |
--------------------------------ttgctgatacatccaacatt---aagtagattttatttatacaaaa----attttcttccttgcatgttctcgtctttatttattttgttcttgttatg--gatttcagCTCTCCTATGTAAAATTGCGGCTTTGAGATCATTTTCTCTGGAGAAGTTACAGTACTGGAGAGAGAGTGCATCTGGCATTAGCAGTCTGGCTTATTTTCT
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0040g01620.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgttta-tataatacgtaatgagaaaataa-gtaagtagtaaaaataaggtaataagcgtgggatatattaat-tgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
|| || | | | | ||| | |||| || | |||||| | | ||| | | | | | | || | | |||||| || || || ||||||| || |||||||||| |||||||| || ||||||||||||| ||||| |||||||| |||||| |||| || || |
------------------------------------------attaacaacat--ggtgcaattttatttaacattactattaatgattttttggcaccgtttgtattttcttgttgttgaaaatatcaattactgacctgcagCACTCCTATGTAAGATTGCGGCTTTGAGATCATTTTCTCTGGACAAATTACACTACTGGAGAGAGAGTGCATCTGGCATGAGCAGTCTGGCTTATTTTCT
upper sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv06s0004g02490.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
||| || ||||| | ||| ||| | ||| | |||| | | | | || ||| | | | | || | || | | | || ||||||| || ||||||||||| || |||||||||| |||||||| || ||||||||||||| ||||| || || ||||||||| ||||| ||||| |
--------------------------ggaacctgtttta-----ggattgattttacagattt----cttatggagtcttcttccacaccatgagttatttct-----catccatccaaattttggctgc-taactttcagCTCTCCTCTGCAAGATTGGGGCATTGAGATCATTTTCTCTGGATAAATTACACTACTGGAGAGAGAGGGCTTCGGGAATGAGCAGCTTGGCATACTTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
tattaat putative branch site (score: 2)
taaaaataaggtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgtttatataatacgtaatgagaaaataagtaagtagtaaaaataaggtaataagcgtgggatatattaattgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA