Sequence
atgc intronic sequence ATGC exonic sequence...tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcctgtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47400.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G08230.1 (Glycine max), 3'ss of exon 3
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcctgtgcaa---tcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
| | | || | | || || | | ||| || | | | | | | || | ||| || | | | | || || ||||||||||||||||||| | ||||||||| ||||||||||||| ||||| || ||||| ||||||||| |||| |||||
-gcagcatcattc-tgatac-aaaacgtatcacaatgtgtattgtttctatttgagttgtgaattgttttgctcagctttctaacgaaatttataaatttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGTTCATCGTTTACCGGTGATGTGGAAGAAGTTGATCCA
upper sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G17150.1 (Glycine max), 3'ss of exon 4
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcctgtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
||| | | | | || | || | |||||| | | | | | | | | | | ||||| | || || ||||||||||||||||||| | ||||||||| ||||||||||||||||||| || || || ||||||||| |||| ||||
-gtattatcttcta-atctatatattgtttctccttatgaactcta----acaattttgcttagctttctaa-cgattttt--------ataaacttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGGTCATCGTTTACTGGTGATGTGGAAGAAGTTGATCAA
upper sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G17190.4 (Glycine max), 3'ss of exon 4
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcct-----gtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
| | || || || | | | | ||| | | ||| | ||||| || | | | ||||||||||| ||||||||| |||||||| |||| |||||||||||||| || || || ||||| ||| || |||||
------------------------gtattgtctactaatcaatatatgttttttgactgtttgtcttcatgaaccattccctaagaatgttgttggctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCATTTACTGGTGATGTTGAAGCTGTTGATCCG
upper sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G17120.1 (Glycine max), 3'ss of exon 3
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcac-atgcttgatcgattcctgtgcaa---tcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
| | | | | |||| | | | || | | | |||| || | | | | ||| || | ||| | || || ||||||||||||||||||| | ||||||||| ||||||||||||| ||||| || || || ||||||||| |||| |||||
-------gtattgtcca--ctagtcaatat-gtattgtttctatttgtgagttgtgaactcaattgtttttgctcagctttctaacaaaatttataaatttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGTTCATCGTTTACTGGTGATGTGGAAGAAGTTGATCCA
upper sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G08240.1 (Glycine max), 3'ss of exon 4
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcga---ttcctgtgcaatc-atcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
|| || | | | || | | || |||| |||| || | ||| || || | | ||| | ||| || || ||||||||||||||||||| | ||||||||| ||||||||||||| ||||| || || || ||||||||| |||| |||||
cattctgataccaaacgtatcacaatg---tgtattatgtctatttatgagttgtg-aactcaattgttttgcccagctttctaacgaaatttataaatttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGTTCATCGTTTACTGGTGATGTGGAAGAAGTTGATCCA
upper sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G35050.4 (Glycine max), 3'ss of exon 4
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcctgtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
| | | | | | | | | || | || | | | || | | || || | || | || | |||| | || ||||||||||||| ||||||| |||||||| |||| |||||||| ||||| || || || ||||||||| ||| ||||
---gtctttcccactagt-ccacacaattttgtttctcctaatgaatccaatattttctttaactttct--aatgagtattgtgaattc--------cagATTTCTACAACTGGAACAGAATCAAGGTTAGGTATTGTGATGGTTCATCATTTACTGGTGATGTGGAAGCAGTGAATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggagtagtatagttcacatgcttgatcgattcctgtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
gcttgat putative branch site (score: 5)
tagtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcctgtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
- -atgaatg
- - - - - - - caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcttg