Sequence
atgc intronic sequence ATGC exonic sequence...tggtagcagaaaatttgggcaccctgatcattattccatcagttccttgtagttgaagaacattttattttcctgacagttttacattatacaaaaatagGCTGTGCAAGGTGGTGAAGTAGGCTTGGTTGTCGATTGTGAATGGGCAGAGCCATTTTCAGAGAAAACAGAAGATCAGGTTGCTGCAGAACGAAGGCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g67220.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AC155376.2_FGT005 (Zea mays), 3'ss of exon 7
------tggtagcagaaaatttgggcaccctgatcattattccatcagttccttgtagttgaagaacattttattttcctgacagttttacattatacaaaaatagGCTGTGCAAGGTGGTGAAGTAGGCTTGGTTGTCGATTGTGAATGGGCAGAGCCATTTTCAGAGAAAACAGAAGATCAGGTTGCTGCAGAACGAAGGCTTG
| | | |||||| ||||| ||||| |||||||| || | | || | ||||| || |||| ||||||||| ||||||||||||||| ||| |||||||||||||||||||||| || ||||||||||||||||||||||| || ||| ||||| || ||||||| |||| ||| |||
gtttcctaccaatattgtatttgg-taccctcatcatctttccatcatttttcta-----gcagtatattttgttcgtctgatggttttacatgttacaaaaatagGCTGCACAAAGTGGTGAAGTAGGCTTGGTTGTTGACTGTGAATGGGCAGAGCCATTTTCTGAAAAACTCGAAGACCAAATTGCTGCGCAACGGAGGATTG
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 7
-------tggtagcagaaaatttgggcaccctgatcattattccatcagttccttgtagttgaagaacattttattttcctgacagttttacattatacaaaaatagGCTGTGCAAGGTGGTGAAGTAGGCTTGGTTGTCGATTGTGAATGGGCAGAGCCATTTTCAGAGAAAACAGAAGATCAGGTTGCTGCAGAACGAAGGCTTG
| || | |||||| ||||| ||||| ||| ||| || || | ||| | ||||| || |||| ||||||||| |||||||||||| || ||||||||||||||||| |||||||| |||||||||||||||||||||||||| || || ||||| || |||||||| | || |||||||
tatttcctaccagtattgtatttgg-taccctcatcatcatttcattgctttctggcagt------atattttgttcatctgatggttttacatgttacaaaaatagGTTGCACAAGGTGGTGAAGTAGGGTTGGTTGTTGATTGTGAATGGGCAGAGCCATTTTCTGAAAATGTGGAAGACCAAATTGCTGCACAGCGGAGGCTTG
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G36890.1 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------tgg-tagcagaaaattt-----gggcaccctgatcattattccatcagttcct---tgtagttgaagaacattttattttcc------tgacagttttacattatacaaaaatagGCTGTGCAAGGTGGTGAAGTAGGCTTGGTTGTCGATTGTGAATGGGCAGAGCCATTTTCAGAGAAAACAGAAGATCAGGTTGCTGCAGAACGAAGGCTTG
||| || | ||| || | || | | | || | || | || | | || | | |||||| || | | ||||||| ||| || |||| |||||||| || | || ||| || ||||||||||||||||||||| || |||||| ||||||| |||||||||| || | | |||
gtatggtagctttttattgtggttcagcaacctaattttgttttattttacttggacctttggctatcggaagatgtctcaaaggttctgttgttgacatctggtacctttatcaatgcatctcaattgcttgttatttaccagtgtgcgtttggtttacat-atattaatctagGAAAGTCAAGGTGGACAAATCGGTTTGTCAGTTGATTGTGAATGGGCAGAGCCAAACTCTGAGAAACCAGAAGACAAGGTTGCTGCGGATAGGCGAATTG
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0220g00070.t01 (Vitis vinifera), 3'ss of exon 6
tggtagcagaaaatttgggcaccctgatcattattccatcagttccttgtagttgaagaacattttattttcctgacagttttac--attatacaaaaatagGCTGTGCAAGGTGGTGAAGTAGGCTTGGTTGTCGATTGTGAATGGGCAGAGCCATTTTCAGAGAAAACAGAAGATCAGGTTGCTGCAGAACGAAGGCTTG
| | | | | | | || | | | | | || || || || | | || || | | || ||| | || | | | ||| |||||| || || ||||||||||||| |||||||||||||| ||| | |||||||| |||| |||||| | |||||||||| | | | ||||
ttgcaattgtcatatacgttacttcagttagcagtaaaacaactc--tgccatttgtgttgttcttgttcttgttactgttctgatgatccttccaccccagGACAAGCAAGGGGGACAAATAGGCTTGGTTGTTGATTGTGAATGGGCTGAGGCTTTTTCAGATAAAATTGAAGATAAAGTTGCTGCAGCAAGGCGTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtagttgaagaacattttattttcctgacagttttacattatacaaaaatagGCTGTGCAAGGTGGTGAAGTAGGCTTGGTTGTCGATTGTGAATGGGCAGAGCCATTTTCAGAGAAAACAGAAGATCAGGTTGCTGCAGAACGAAGGCTTG
tcctgac putative branch site (score: 2)
agttttacattataca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtagcagaaaatttgggcaccctgatcattattccatcagttccttgtagttgaagaacattttattttcctgacagttttacattatacaaaaatagGCTGTGCAAGGTGGTGAAGTAGGCTTGGTTGTCGATTGTGAATGGGCAGAGCCATTTTCAGAGAAAACAGAAGATCAGGTTGCTGCAGAACGAAGGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG