Sequence
atgc intronic sequence ATGC exonic sequencegtactgcatggcttggctctgtttcttttttgtgaaaaaaaatattcttatctttcaatgatatttatattcacattactgaagGCAATAGAAGTGGTTGACCTGGACCAGAAGACAAAAATGGTTACTGAGCTTGATGGCCATATCATGAGATGCGTGCGTGATCAAAATGGAAACCATGTTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62650.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G04060.2 (Glycine max), 3'ss of exon 6
-----------------------------gtactgcatggcttggctctgtttcttttttgtgaaaaaaaatattcttatctttcaatgatatttatattcacattactgaagGCAATAGAAGTGGTTGACCTGGACCAGAAGACAAAAATGGTTACTGAGCTTGATGGCCATATCATGAGATGCGTGCGTGATCAAAATGGAAACCATGTTA
| | | | ||||||||| || | ||| || | | ||| ||| || || ||| |||| | || |||| |||||||| ||||| ||||||||||||| ||| |||||| || |||||||| |||||||| | || ||||| ||||| ||||| || ||||| |
gtattcacagctatgggtgctagtatttgacatttctatgtatggctctgtatccataatgttctgaaga----tgccatccttctat-atttttttatt-gtgct-cttcagGCCATAGAAGTTGTTGATCTGGACCAGAAGATAAAGATGGTTCAAGAACTTGATGGAAATATCATGCGTTGTGTGCGAGATCAGAATGGCAATCATGTAA
upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
--------------gtactgcatggct-tggctctgtttcttttttg--tgaaaaaaaatattcttatctttcaatgatatttatattcacattactgaagGCAATAGAAGTGGTTGACCTGGACCAGAAGACAAAAATGGTTACTGAGCTTGATGGCCATATCATGAGATGCGTGCGTGATCAAAATGGAAACCATGTTA
|| | || | | | || || | || ||| | | | | |||| ||| || || | | || ||||||||||||| ||||| | ||||| |||| ||||||||| ||||||||||| ||||||||| |||| ||||||||||| |||||||||||||| |
gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaa-atgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgaaaaaaaatattcttatctttcaatgatatttatattcacattactgaagGCAATAGAAGTGGTTGACCTGGACCAGAAGACAAAAATGGTTACTGAGCTTGATGGCCATATCATGAGATGCGTGCGTGATCAAAATGGAAACCATGTTA
aaaaaaaatattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgcatggcttggctctgtttcttttttgtgaaaaaaaatattcttatctttcaatgatatttatattcacattactgaagGCAATAGAAGTGGTTGACCTGGACCAGAAGACAAAAATGGTTACTGAGCTTGATGGCCATATCATGAGATGCGTGCGTGATCAAAATGGAAACCATGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG