Sequence
atgc intronic sequence ATGC exonic sequence...taggtgtaatttcttgtattacattttcattatttacccctgagaggtcttggcttggggagtcgatttcagttggactgatttaattttaacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g29720.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G106703_T01 (Zea mays), 3'ss of exon 9
taggtgtaatttcttgtattacattttcat-tatttacccctgagaggtcttggcttggggagtcgatttcagttggactgatttaattttaacc-tggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG
|| | ||| | | | |||| || | | || || ||| | | | | | | | || | | | | | || | || | |||||| |||||||| ||||||| |||||||||| || || |||||||| ||||| ||||| ||||||||||| |||||| |||| |||||||||||||| |||
-agttttaactgatag-attatatagtggtatagataaaggtgatatataatatactcgtaactgatttgctgctcgcttatatttttgttgtctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACGTGCTGGTCCATCAGTTGGTATCGTCGTTTCCTTCTACGAGGTTGTCAAG
upper sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G059018_T01 (Zea mays), 3'ss of exon 9
taggtgtaatttcttgtattacattttcattatttacccctgagaggtcttggcttggggagtcg--atttcagttgg--actgattta-attttaacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG
| | | | || | ||| | ||| | || | | | | | | ||| || | || ||| ||| | ||||||| |||||||| |||||||| ||||| |||| ||||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||||||||| |||
-----attcctcccttagttctactttagtaattggtttggtaaggggcatctataatgtacccataattgtgatttgttgcttgcttatattgttctctggcagGTCTGGAGGCATGAAAGGTCTGTTCGCCGGCGTTGGCCCACGTGTTGCACGCGCTGGTCCATCAGTTGGTATTGTCATTTCCTTCTACGAGGTTGTCAAG
upper sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G13050.1 (Glycine max), 3'ss of exon 9
taggtgtaatttcttgtattacattttcattatttacccctgagaggtcttggcttggggagtcgat--ttcagttggactgatttaattt-taacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG
| |||| | | | ||||| | ||| | | || | | | | | || || | || ||| |||| | | || ||| ||||||| ||||||| ||||| || |||||||||||||| || | ||||| ||||| || |||||||| || ||||| || || || ||||| |||
-acttgtagt--cagggtaaacattgtttgaattgatcagtgtgttgatataaatgatcaatgttatgctttatctgaactaatttttcatatcttctttcagAGATGGAGGTTTGAAAGGATTGTTTACGGGTGTTGGTCCACGAGTTGGTCGAGCAGGCCCCTCCGTTGGAATTGTGATTTCATTTTATGAAGTTGTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcttggcttggggagtcgatttcagttggactgatttaattttaacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG
ttttaac putative branch site (score: 2)
actgatttaattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggtgtaatttcttgtattacattttcattatttacccctgagaggtcttggcttggggagtcgatttcagttggactgatttaattttaacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG
- - - - -tttcttg
- - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - tggcttg