Sequence
atgc intronic sequence ATGC exonic sequence...accttctgaactacattctttattattttgctcttttttaatcttggacatcttacattctatatttcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os01g10050.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 2
accttctgaactacattctttattattttgctcttttttaatcttggacatcttacattctatat-ttcctgatccaagatacttaacttccattgtg-cagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
| | | ||| || |||| ||||| | | | | | ||| ||| || || | ||| || ||| | || |||||||||| |||||||| || ||||||||||| ||||| |||||||| |||||||| || ||||||||||| |||||| |||| || || || ||||||||
agtgttccttttgcatgtagcat-gcattgcacttttctgctgtgtgggaccttcatatctgcatatttatagctttggatgct-gactgttgtggtttcagAATATGTGTTGCAAGAGATCACAAAAGCTGGTTTTGTGGAACCTACCCCTATCCAATCGCAAGGTTGGCCGATGGCATTGAGAGGCCGCGACCTTATTGG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 1
accttctgaactacattcttt-attattttgc------tcttttttaatcttgg-acatcttacattctatatt-tcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
| | || ||| | | ||||| |||| | || | || ||| | ||| | | | | | ||||| ||| || | |||||||||| || ||||||||||||||||||| ||| |||||||| || || || |||||||||||||| ||||| ||| ||| |||||||| || ||
-----attgattatattgtatgattatcttgcaaaaaattttatcagattatgggatgacttgtttcaaacagtgtactgatttttcggccttggttt----aatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTAATAGG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
accttctgaactacattctt-tattattttgctcttttttaatcttggacatcttacattctatatttcctgatccaagatacttaacttccatt--gtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
| |||| || || | || | || | | | | || | || | | | | | | | | | | || | |||||||||| |||||||||||||||||||||| ||| |||||||| || || || |||||||||||||| ||||| ||| ||| |||||||| || ||
tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgta---ctgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
accttctgaactacattcttt-attattttgc-----tcttttttaatcttggacatcttacattctata---tttcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
| | || ||| | | ||||| |||| | || | | | | || | || | | | | ||||| ||| || | |||||||||| || ||||||||||||||||||| ||| |||||||| || || || |||||||||||||| ||||| ||| ||| |||||||| || ||
-----attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggttt----aatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------accttctgaactacattctttattattttgctcttttttaatcttggacatcttacattctatatttcctgat---ccaagatacttaacttcc--attg-tgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
| ||| ||| || ||| | || | | | | || | | | || | | | | ||||| ||| || | | || |||| |||| |||| ||||||||| |||| ||| || ||||| ||| |||||||| ||||| || ||||| || ||||||||||| ||| ||||||||||||||| ||
gtaaactcttgaatttggcaatcatgtagagcttgtga-ttagtttcacttacatgtcttagatgtatgatgtagcatatat-gcctgttttatttttggatatacctactgatatagtttcctgattggctcagATTATGTTTTGGAAGAGGTTAAGAAGGCTGGTTTTACTGAACCTACGCCTATACAATCTCAGGGGTGGCCAATGGCTATGAAGGGACGTGATCTTATCGG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
-accttctgaactacattctttattattttgctctttttta-atcttggacatcttacattctatatttcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
| ||| || |||| || | | | ||| || |||| || ||| | | | ||| | || | | || ||| | |||||||||| |||||||||||||||||||||| |||| |||||||| || ||||| ||||||| ||||||||||| ||| ||| |||||| | |||||
aaatcagtgactggcaacctttcttgagaagttatgctttggatgatggatattttaaaattgaagttt--taattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggacatcttacattctatatttcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
acttaac putative branch site (score: 3)
cttccatt CT-rich tract
ttacattctatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accttctgaactacattctttattattttgctcttttttaatcttggacatcttacattctatatttcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG
-ccttctg
- - - - aactaca
- - - - - - - - - - - - -ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - -cttacat
