Sequence
atgc intronic sequence ATGC exonic sequence...tataattgcattcatgccagttttacaagatcgcactcgaatcgattaattcttggacagatctgttaattcttctgatccttcgcttgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC
Basic information
| species | Oryza sativa |
| transcript | LOC_Os11g44790.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g44790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G026311_T02 (Zea mays), 3'ss of exon 4
---------------tataat--tgcattcatgccagttttacaagatcgcactcgaatcgattaattcttggacagatctgttaattcttctgatccttcgcttgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC
| |||| | |||| || | || || | | | ||| || | || | || | ||||| | || |||| |||||| ||||| | || |||||||||||||||||||||||||||||||||||||||| || ||||||||| ||||| |||||||| ||| | |||||||| |||| ||||||||||| ||
gtaagactatgaagctttaatgatccatttatatttatcttggaactttggaatcgcat-gtatattgtttctatgagtctgt-atctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC
upper sequence: LOC_Os11g44790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G42650.1 (Glycine max), 3'ss of exon 3
tataattgcattcatgccagttt-tacaagatcgcactcgaatcgattaattcttggacagatctgttaattcttctgatccttcgcttgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC
| || ||||| |||| | || | | | | | || | ||| | || || | ||| | || | || | |||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| || || | || ||||| ||||||| || || || |
attccttttgttcatctttgtttctccactagagaaatttgttacatgtgtccttct-tgaaccttttggtgtttcatactgatctttaactaaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
upper sequence: LOC_Os11g44790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G11630.1 (Glycine max), 3'ss of exon 3
tataattgcattcatgccagttttacaagatcgcactcgaatcgattaattcttggacagatctgttaattctt-ctgatccttcgctt--gtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC-
| ||| |||| | || || | || | | ||| | | || |||| | ||| | | | ||| | ||||| | | || | |||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| || || |||| ||||| ||||||| ||| || || |
-agtattacatt--ttccttttgttcatctttgttctccacttgagaaatttgtt-acatgtgtccttgttcatactgatgtgtaagtgtaactaaatttcaggTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACTGAGTTGAACAAAGACCACAATGAGATTCTAGAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattcttggacagatctgttaattcttctgatccttcgcttgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC
ttctgat putative branch site (score: 3)
ctctc putative PPT
ttaattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataattgcattcatgccagttttacaagatcgcactcgaatcgattaattcttggacagatctgttaattcttctgatccttcgcttgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- -aattgca
- - - - - ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - attcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtta
