Sequence
atgc intronic sequence ATGC exonic sequencegttagtttctctttacatgctttacacatttgttattatatgttgatcttaatctgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os03g20880.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------------------------------------------------gttagtttctctttacatgctttacacatttgttattatatgttgatcttaatc-tgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
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gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
upper sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
-gt-tagtttctctttacatgctt-------tacacatttgttattatat--gttgatct------------taatctgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
|| || ||| || |||| | | || | ||| || ||| || | || | || |||| | | || ||||| ||||||||||||||||| |||||||| ||| ||||||| ||| | |||||||||||||| |||||||| |||||||| || |||||||||| || |||||||
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
upper sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G02980.1 (Glycine max), 3'ss of exon 2
-----------------------gttagtttctctttacatgctttacacatttgttattatatgttgatcttaatctgttatgatgtttttttgtg-tagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
|| ||| || | || || | |||| | | || | ||||||| | | |||| |||||||||| |||||||| ||||| ||| ||||||| || |||||||||||||||| || ||||| ||| | || || | |||||||| || ||||| |
aattttaaagtgttttgaaaaaagtgtgttgctatcatatctctgtatttacctgtttctggtcacttat-tccgtctgttacttcaaatatatgtggcagGTTGAAAACCAAGAAGGGGTTGCAAATTTTGATGAAATCCTTGCAAATTCAGATGCATTTATGGTGGCACGTGGTGACCTTGGAATGGAAATTCCAATAG
upper sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G35110.2 (Glycine max), 3'ss of exon 3
-----------------------gttagtttctctttacatgctt-tacacatttgttattatatgttgatcttaatctgttatgatgtttttttgtg-tagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
|| ||| || | | || || || | |||| | | || | ||||||| | | |||| |||||||||| |||||||| ||||| ||| ||||||| || |||||||||||||||| || ||||| ||| | || || | |||||||| || ||||| |
gatttaaaagtattttgaaaaaagtgtgttgctatc-atatctttgtatttacctgtttctggtcacttattctg-tctgttacttcaaatgtatgtggcagGTTGAAAACCAAGAAGGGGTTGCAAATTTTGATGAAATCCTTGCAAATTCAGATGCATTTATGGTGGCACGTGGTGACCTTGGAATGGAAATTCCAATAG
upper sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G56350.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------gttagtttctctttacatgctttacacatttg--ttattatatgttgatcttaatctgttatgatgttttt--ttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
| ||| | || | |||| | | ||| | |||| | | || ||| | ||||| ||| ||||| || || ||||||||||| || ||| ||||||| || | | |||||||| ||||||||| |||| ||||||||| |||| ||||| ||||| ||||
gtatgttaaatcaaagctctctttttagttccggaaactacaggatcaaatctttaggttgtgatggttttgtgctatcttctttttgattgattagGTCGAGAACCAAGAAGGTGTGGCAAATTTTGATGACATTTTGGTCAATTCAGACGCTTTCATGATTGCTAGAGGAGATCTGGGCATGGAAATCCCGATTG
upper sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g07600.t01 (Vitis vinifera), 3'ss of exon 2
----gtta--gtttctctttacatgctttacacatttgttattatatgttgatcttaatctgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
||| ||| | || || | ||||| || | | | | | || || ||| | |||||||||||||||| |||||||||||| ||||||| || ||||||| |||||||| || ||||| || || || || | |||||||| ||||| ||||
gtatgttgaggttgcaaagaactctgttgaagtatttgcatttttgggaaggatatgactaattttgtgatttg-----gcagGTTGAAAATCAAGAGGGTGTTGCTAATTTTGATGAAATTCTTGCAAACTCAGATGCATTTATGGTGGCCAGGGGTGACCTTGGAATGGAAATCCCCATTG
upper sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g00130.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------gttagtttctc--tttacatgctttacacatttgttattatatgttgatcttaatctgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
||| || | |||||| | ||| | ||| | || || || || | | | ||| |||| ||||||||||||||||||||| || || ||| ||||||| || |||||||||||||||| || ||||| ||| |||| ||| |||||||||| |||||||| |
gtagcttgatttttacagaaaaaaattgaaggtttaattaagttgtgaatttacagtagagtaatctttctcatt-tctgatgcctggtatttgctttaaaatttgtttg-gtagGTTGAAAATCAAGAAGGGGTGGCAAATTTTGATGAAATCCTTGCAAATTCAGATGCATTTATGGTGGCACGAGGTGATCTGGGAATGGAAATCCCAATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacacatttgttattatatgttgatcttaatctgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
tcttaat putative branch site (score: 3)
tgttttttt putative PPT
ttattatatgttgatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttctctttacatgctttacacatttgttattatatgttgatcttaatctgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
