Sequence
atgc intronic sequence ATGC exonic sequence...cttataccctcaagaattaagtttgtgacgttttttttctaacatttgtaatgtggtgtggaagtcttttgtatatgaaattttgcagtttcttttgtagGTAACTGCAGTCGGTCTAAACACTGAGTGGGGCTTATTGATGGCCAGCATCTCAGAAGACAACAATGAAGAAACTCCACTACAG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os02g08018.1 |
| intron # | 8 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g08018.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G892495_T02 (Zea mays), 3'ss of exon 1
--cttataccctcaagaattaagtttgtgacgttttttttctaacat---ttgtaatgtggtgtggaagtcttttgtatatgaaattttgcagtttcttttgtagGTAACTGCAGTCGGTCTAAACACTGAGTGGGGCTTATTGATGGCCAGCATCTCAGAAGACAACAATGAAGAAACTCCACTACAG
| | ||| | | | || | |||||| ||| ||| || |||| || |||||| |||||| ||| ||||| |||| ||||||| || || || || ||||| || ||||| ||||| ||||||||||| |||||||||||||||||||||||||| || |||
cagtggtgcccccccca--cacacacacagagtctaacaattaacatgctttgcaatcaggcctggatgt-ttttgtgtatgaacatttccagtt--ctttgcagGTAACGGCTGTTGGCCTTAACACCGAATGGGGTTTATTAATGGCCAGCATTTCAGAAGACAACAATGAAGAAACTCCTCTGCAG
upper sequence: LOC_Os02g08018.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 11
cttataccctcaagaattaagtttgtgacgttttttttctaacatttgtaatgtggtgtggaagtcttttgtatatgaa---attttgcagtttcttttgtagGTAACTGCAGTCGGTCTAAACACTGAGTGGGGCTTATTGATGGCCAGCATCTCAGAAGACAACAATGAAGAAACTCCACTACAG
|| | | | ||| | ||| | | |||| | || | | ||| | | | | ||||| | | || | |||||||||||| || ||| |||| ||||||||||| || |||||||| || |||||||| || | ||||| |||||| |||||
tttgaattttttatgatt---ctagtggcatattttaagcacacgaaacaaattttttcagaatgttactacaccctgacttattttttactgtcatctgtagGTAACTGGTGTTGGTATAAATACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAGGATACTGGAGAAGAGACTCCATTACAG
upper sequence: LOC_Os02g08018.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
cttataccctcaagaattaagtttgtgacgttttttttctaacatttgtaatgtggtgtggaagtcttttgtatatgaaattttgcagtttcttttgtagGTAACTGCAGTCGGTCTAAACACTGAGTGGGGCTTATTGATGGCCAGCATCTCAGAAGACAACAATGAAGAAACTCCACTACAG
|| | | | | | || |||| ||| || | || | || || | | | | ||| | | |||| | || ||||| |||| || || | |||||||||||||| || |||||||| || ||||||||||| | ||||||||||||| | |||
-gtaaatctttgaaactt----ttgtcctgttcttagttctgttttcacatagttgt-tcatacttcctagta-gttattctttgtgagtgtttcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtaatgtggtgtggaagtcttttgtatatgaaattttgcagtttcttttgtagGTAACTGCAGTCGGTCTAAACACTGAGTGGGGCTTATTGATGGCCAGCATCTCAGAAGACAACAATGAAGAAACTCCACTACAG
tttcttttgt CT-rich tract
ttttgtatatgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttataccctcaagaattaagtttgtgacgttttttttctaacatttgtaatgtggtgtggaagtcttttgtatatgaaattttgcagtttcttttgtagGTAACTGCAGTCGGTCTAAACACTGAGTGGGGCTTATTGATGGCCAGCATCTCAGAAGACAACAATGAAGAAACTCCACTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - -tgtgacg
- - - - - - - - - - - - - - - - - - - - -acatttg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca
