Sequence
atgc intronic sequence ATGC exonic sequencegtgagtagaagttgaattgacactgcatagacattcgtaggttgtgatattcaaatgtgtgtgatgctatttgcagGACTTCTTTAAAAAACGTGGTGTTGCTGTCATGTCAGTAACAGAACTATTTAATTTTGTGATTGATCAAAATATTGCTGATGAAGATGTTGATCATTACC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g06820.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 8
gtgagtagaagttgaa-ttgacactgcatagacattcgtaggttgtgatattcaaatgtgtgtgatgctatttgcagGACTTCTTTAAAAAACGTGGTGTTGCTGTCATGTCAGTAACAGAACTATTTAATTTTGTGATTGATCAAAATATTGCTGATGAAGATGTTGATCATTACC--------
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gtaagtgaaagttgaagcttacttcgcatatatactcataaatttctgtgaccga-tatgttcaatatt--ttgcaggacttctttaaaaaacgtggtgttcctgtcatgacagTAACGGATTTGTTTAATTTTGTTATTGATCAAAGCATTTCTGATGAAGATGTTGATGATTACCTGGAAAAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G120329_T02 (Zea mays), 3'ss of exon 9
gtgagtagaagttgaa-ttgacactgcatagacattcgtaggttgtgatattcaaatgtgtgtgatgctatttgcagGACTTCTTTAAAAAACGTGGTGTTGCTGTCATGTCAGTAACAGAACTATTTAATTTTGTGATTGATCAAAATATTGCTGATGAAGATGTTGATCATTACC
|| ||| |||||||| | || ||||| | | || || || | | | | ||| || | |||||||||||||||||||||||||||||| |||||||| ||||||| || | ||||||||||| |||||||||| ||| ||||||||||||||||| ||||||
gtaagtgaaagttgaagcttacttcgcatatatactcataaatttctgtgaccga-tatgttcaatatt--ttgcagGACTTCTTTAAAAAACGTGGTGTTCCTGTCATGACAGTAACGGATTTGTTTAATTTTGTTATTGATCAAAGCATTTCTGATGAAGATGTTGATGATTACC
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 10
gtgagtagaagttgaat-tgacactgcatagacattcgtaggttgtgatattcaaatgtgtgtgatgctatttgcagGACTTCTTTAAAAAACGTGGTGTTGCTGTCATGTCAGTAACAGAACTATTTAATTTTGTGATTGATCAAAATATTGCTGATGAAGATGTTGATCATTACC
|| ||| |||||| | | || ||||| | | || || || | | | | ||| || || |||||||||||||||||||||||||||||| |||||||| ||||||| || | ||||||||||| |||||||||| ||| ||||||||| ||||||| |||| |
gtaagtgaaagttgtaccttacttcgcatatatactcataaatttctgtgaccga-tatgttcaatact--ttgcagGACTTCTTTAAAAAACGTGGTGTTCCTGTCATGACAGTAACCGATTTGTTTAATTTTGTTATTGATCAAAGCATTTCTGATGAAGGTGTTGATGATTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgcatagacattcgtaggttgtgatattcaaatgtgtgtgatgctatttgcagGACTTCTTTAAAAAACGTGGTGTTGCTGTCATGTCAGTAACAGAACTATTTAATTTTGTGATTGATCAAAATATTGCTGATGAAGATGTTGATCATTACC
atattcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtagaagttgaattgacactgcatagacattcgtaggttgtgatattcaaatgtgtgtgatgctatttgcagGACTTCTTTAAAAAACGTGGTGTTGCTGTCATGTCAGTAACAGAACTATTTAATTTTGTGATTGATCAAAATATTGCTGATGAAGATGTTGATCATTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG