Sequence
atgc intronic sequence ATGC exonic sequence...aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttttttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g43860.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
-----aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttt-tttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
| ||||||||| || | | | || | | | ||| | | | || || ||| || ||| | |||||| | ||||| |||||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| ||||| || ||||
ataattaatcattttgt--ggcaagagcaggttgtta-tcattctctgttttttccctctttcgaatggttcta---aattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 2
aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaa-aatgtttttttttct-----tgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
||| || || || || ||| || | ||| || | ||| | | | || || |||| || | ||||| |||| ||||| || | || ||||| ||||| |||||||| || || ||||| || || ||||||||||||||||| |||||||| ||||| |||| |
------gttttttcatggtgtgtgattttttatgtgatggagcttatcatctgctattatacatttacaactgacaattttgatattttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC
upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1
aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttttttt-------tcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
| | ||| |||| | | || ||| | | ||| | || | | || | | | ||| |||||||||| | | |||||| | || ||||| ||| | || ||||| ||||| |||||| | ||||| ||||| || || |||||||||||||||||||||||||| ||||| | || |
----cttcttgattataaaatggatttttttttctctatatggagaggtttgttgg---atgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 1
-----aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttttttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
|| || ||| || ||| | || ||| |||| | | | | | | | ||| | || || | | || | |||||| | || ||||| ||| | || ||||| ||||| |||||| | || || ||||| || || |||||||||||||||||||||||||| ||||| | || |
attgtaaaatggattttttttc--gta-ttttttttatgtggagaagtttgt-tggatgtagtacatttatggttttgatgtttct-tatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G06890.1 (Glycine max), 3'ss of exon 1
aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcc-taaggcaatttt---ttttacttaataaaaaaatgtttttttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
| | ||| || || || | || | | |||| | | | || || || | || | | | | || ||| || ||||| |||| ||||| || | || ||||| ||||| |||||||| || || ||||| || || ||||||||||||||||| |||||||| ||||| | || |
----cccctagttcatggtgtgtgatttctgatgtgatagagcttatctgctatgatacatttacaacttacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttcctaaggcaattttttttacttaataaaaaaatgtttttttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
acttaat putative branch site (score: 4)
tgtttttttttcttgc putative PPT
aattttttttacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttttttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG