Sequence
atgc intronic sequence ATGC exonic sequence...tgttcttaatttttgaaatctatatattcatcctgcaatgcattatattcaaaccaaggtgaatttgtttataaaatttttttgaattgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g37880.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g37880.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G026043_T01 (Zea mays), 3'ss of exon 4
tgttcttaatttttgaaatctatatattcatcctgcaatgcattatattcaaaccaaggtgaatttg-tttataaaattttt--ttgaattgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
| | |||||| | | || | | || ||| | | | | | |||| | ||| ||| ||||| || | || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| || ||||
---tataaattttaactttttttaactaccaccggcagGCTTTGGGGTGCCTTCTATATAGAATATAATTTGTAACCTTTTTCTTTTTACCTACCACTGGCAGGCTTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAATCCAAGTTGCAGATACTCAATGGCAATTATCGTATCCCTGAGC
upper sequence: LOC_Os02g37880.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G026043_T01 (Zea mays), 3'ss of exon 4
tgttcttaatttttgaaatctatatattcatcctgcaatgcattatattcaaaccaaggtgaatttg-tttataaaattttt--ttgaattgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
| | |||||| | | || | | || ||| | | | | | |||| | ||| ||| ||||| || | || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| || ||||
---tataaattttaactttttttaactaccaccggcagGCTTTGGGGTGCCTTCTATATAGAATATAATTTGTAACCTTTTTCTTTTTACCTACCACTGGCAGGCTTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAATCCAAGTTGCAGATACTCAATGGCAATTATCGTATCCCTGAGC
upper sequence: LOC_Os02g37880.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G051079_T01 (Zea mays), 3'ss of exon 4
tgttcttaatttttgaaatctatatattcatcctgcaatgcattat--attcaaaccaaggtgaatttgtttataaaatttttttga--attgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
|| || | | | | ||| || ||| || || ||| | | | | || | || | |||||||| | || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||| |||| ||||||||||||| ||| || ||||
---gctcaagtatcacattgtatttaa-cattaatcattgagctattggtgaagagtgaagtaatttgtaacctcttctttttttggttacctaccactggcagGCTTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGACGGAGAATCCAAGTTGCAGGTACTCAATGGCAATTATCATATCCCTGAGC
upper sequence: LOC_Os02g37880.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G32850.1 (Arabidopsis thaliana), 3'ss of exon 4
tgttcttaatttttgaaatctatatattcatcctgcaatgcattatattcaaaccaaggtgaatttgtttataaaatttttttgaattgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
|| | ||| | | | | || | | ||| || || | || ||| |||| ||| || || | | |||| | || || || | | | | |||||||| |||||| ||||||||||||||| || ||| |||| || | || || |||||||||||||||||
-----gtatgtgatgacactttttcaatctctccagattgc----taatctatttggttgaaacttgaaagtaaaggtttgttt--ttaaaaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
upper sequence: LOC_Os02g37880.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 5
----------tgttcttaatttttgaaatctatatattcatcctgcaatgcattatattcaaaccaaggtgaatttgtttataaaattt---ttttgaattga-catttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
| | ||| ||||||| || || | | || ||| || || || || ||| || | |||| | | ||| |||||| | |||||||| || | | | |||||||||||||| |||||||||||||| || || ||||| || || | ||||| || || || ||||||||
gtaagtcagttatactttatttttgt--tcaatgagtctgggttatgatttgctattcaagaagttttctgtgctttttaatacaaccaaaacctgaaattcatctttttgcagGCGCTTGGGTGCCTCCTCTTTCGCATATGCTACTTCAAATCTGCATTTGATGGTGAATCAAAGTTACAAATCTTAAATGGAAACTACCGCATTCCAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcaaaccaaggtgaatttgtttataaaatttttttgaattgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
aattgac putative branch site (score: 3)
tgaatttgtttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttcttaatttttgaaatctatatattcatcctgcaatgcattatattcaaaccaaggtgaatttgtttataaaatttttttgaattgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
tgttctt
- - - - - - - - - - - - - - - tcctgca
- - - - - - - - - - - - - - - - - - -atgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - aaaccaa