Sequence
atgc intronic sequence ATGC exonic sequence...gtggattttttaagtggaaaaagaaaaggcattatacttgtcagctagcaatatatttttacaggtgtacttatatgggtttcaacttttttttttctagTGGATCAATTGGTGCAAGGCTATCTACTGATGCTTTGAACGTGAAGCGCCTCGTTGGGGACAATTTGGCACTAAATTTCCAGACTTTGTCGACCATAATA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g35030.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g35030.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G086730_T01 (Zea mays), 3'ss of exon 8
----gtggattttttaagtggaaaaagaaaaggcattatacttgtcagctagcaatatatttttacaggtgtacttatatgggtttcaacttttttttttctagTGGATCAATTGGTGCAAGGCTATCTACTGATGCTTTGAACGTGAAGCGCCTCGTTGGGGACAATTTGGCACTAAATTTCCAGACTTTGTCGACCATAATA
|| | |||||| || | || ||| | || || | || | | |||| | ||| || || ||||| || |||| ||| |||||||||||||||||||| ||||| || ||||| ||||||| ||||| || |||||||||||||| ||||| ||| | |||||||| || || | |||
gtgtgttggtttttttttattctcaaaacaatctattttgct-gttatcttaagaaacatttctccagctg-------gtgtatttcattttcttttattccagTGGATCAATTGGTGCAAGACTATCAACCGATGCCATGAACGTTAAGCGGCTTGTTGGGGACAATTTAGCACTCAATGTGCAGACTTTATCAACTGTCATA
upper sequence: LOC_Os01g35030.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 8
gtggattttttaagtggaaaaagaaaaggcattatacttgtcagctagcaatatatttttacaggtgtacttatatgggtttcaacttttttttttctagTGGATCAATTGGTGCAAGGCTATCTACTGATGCTTTGAACGTGAAGCGCCTCGTTGGGGACAATTTGGCACTAAATTTCCAGACTTTGTCGACCATAATA
|||| | |||| || | |||| | || | || | | | || |||| | ||| || || |||||| || ||||||||||||||||||| ||||||| || || | || || || || ||||| ||| |||||| | | || | |||
-------------gtgggtctataaaaaat----taatggtcaagt----gcttaatcttgttgat-tgtctaactgggaa--atttttgcttatttcagTGGAGCAGTTGGTGCAAGGCTATCTACCGATGCTTCGAGTGTTCGCAGTCTGGTGGGTGATGCATTGGCCCTAGTAGTCCAGAACCTTACAACAGTCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagcaatatatttttacaggtgtacttatatgggtttcaacttttttttttctagTGGATCAATTGGTGCAAGGCTATCTACTGATGCTTTGAACGTGAAGCGCCTCGTTGGGGACAATTTGGCACTAAATTTCCAGACTTTGTCGACCATAATA
tttcaacttttttttt CT-rich tract
tttcaacttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggattttttaagtggaaaaagaaaaggcattatacttgtcagctagcaatatatttttacaggtgtacttatatgggtttcaacttttttttttctagTGGATCAATTGGTGCAAGGCTATCTACTGATGCTTTGAACGTGAAGCGCCTCGTTGGGGACAATTTGGCACTAAATTTCCAGACTTTGTCGACCATAATA
- - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - -atacttg
- - - - - - - - - - - - - - - - - - - - - -gctagca