Sequence
atgc intronic sequence ATGC exonic sequence...aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttttgccaacttttaggtaagatttgtaacttttccacctgctgtttacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g44040.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 7
aatggtagtttccttataatgtcagtcaccat-tattttcagttgctgtcttttgc-caacttttaggtaagatttgtaacttttccacctgctgtt-------tacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
||| ||| || | || || | | |||||||| | || | | || || |||| || | || ||| | || |||| | |||||||| ||||||||||| || |||||||| || || || |||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||
--------attcattagaaacttagaaactacattctttcagttttaattttgtctgttatttctaagtaatggtt-catctgttcaagcttttgttccatctgttcagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT
upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G25780.2 (Glycine max), 3'ss of exon 7
aatggtagtttccttataatgtcagtcaccat-tattttcagttgctgtcttttgc-caacttttaggtaagatttgtaacttttccacctgctgtt-------tacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
||| ||| || | || || | | ||||||||| | || | | || || |||| || | || ||| | || |||| | |||||||| ||||||||||| || |||||||| || || || |||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||
--------attcattagaaacttagaaactacattttttcagttttaattttgtctgttatttctaagtaatggtt-catctgttcaagcttttgttccatttgttcagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT
upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 7
aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttttgcc-------aacttttag----gtaag--atttgtaacttttccacctgctgttta-cagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
| || | || || | | || |||| | || ||| | | | | || ||| | | || | | | || | || |||| ||||| |||| |||||||| ||||| ||||| || | || |||||||| ||||| ||| | || |||||||| ||||| ||||||||||| ||||| ||||
-gcaagtttctcttgattattcccaatatgatcatttcctttttctggccggtaactgtatggagctcttactgccgctggctatatacagtctcatgacttactttttaacagGTTTTGTTCTTAATGTATCACTACTTTGCTGCGGCCGAGATATACAACGCAATCCGTATCTTTATTGCTGCTTATGTTTGGATGACTGGTTTTGGAAACT
upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------------aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttt---tgccaacttttaggtaag---atttgtaacttttccacctgctgtttacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
| | || | | | | || | || | || || || | | | | | ||||| || | | |||| | |||| | ||| ||||| || ||| | ||||| || || ||||| || |||| ||||| |||||||| | ||||||||||||||||| |||||||||||||| ||||||||||
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctga-gttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtc-----tttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 1
---------aatggtagtttccttataatgtcagtca--ccattattttcagttgctgtcttttgccaacttttaggtaagatttgtaacttttccacctgctgttta-cagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
|| | || || || || | | ||||| || ||| | | | || || | || || | | | | | || |||| ||||| || ||| ||||||||||||| ||||| || | || |||||||||||||||||||| || |||||||| ||||||||||||||||||||||| ||||
gttttactttatttttattatctattattgcttgcaatgccattgttacatagtgcaatttgcctcaaataattttctgagcttggatttgtcttctttttctttttaacagGTTCTATTTCTAATGTACCACTACTTTGCTGCTGCGGAGATATACAATGCAATTCGTGTCTTTATTGCTGCATATGTCTGGATGACTGGATTTGGAAACT
upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S74_21V6.1 (Physcomitrella patens), 3'ss of exon 6
----aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttttgccaacttttaggtaagatttgtaacttttccacctgctgtttacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
| | || || | | || | | | ||| || | || | | || ||| | || || | | | || || ||| |||||||| || | ||||| ||||| || | || | || | |||||||| ||||| || |||||||||||||| || |||||||| || ||||| ||||
tgcgacttgtgaattgttaagaagaaagtttatcgttagttcga--tgatttaacctgttcactga-atttataatgtattatttacttgtctaaaattt-cagGTCCTTTTCCTTATGTATCACTACTTCGAAGCAAAGGAGTTTTACAATGCTATTCGGGTGTTCATTGCTGCCTACGTTTGGATGACGGGTTTTGGCAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcttttgccaacttttaggtaagatttgtaacttttccacctgctgtttacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
ttgtaac putative branch site (score: 2)
cttttccacctgct CT-rich tract
aactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttttgccaacttttaggtaagatttgtaacttttccacctgctgtttacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC