Sequence
atgc intronic sequence ATGC exonic sequencegtaggattcttgtttttgcatttggtgtctactcgtgttaccctttattttattttttcttatgtcttcaaggacagGTTTTATGTGACAGGCACTATGGAGGAATTAACTACCCGGTTGGTGGAGTTGGTGGGATTGCCAAGTCTTTGGCAGAAGGGCTTGTTGATCAAGGCAGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G06820.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G06820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g36440.1 (Oryza sativa), 3'ss of exon 5
gtaggattcttgtttttgcatttggtgtctactcgtgttaccctttattttattttttcttatgtcttcaaggacagGTTTTATGTGACAGGCACTATGGAGGAATTAACTACCCGGTTGGTGGAGTTGGTGGGATTGCCAAGTCTTTGGCAGAAGGGCTTGTTGATCAAGGCAGTG
||| | || | | | | | || || | | || | ||| | || ||| | | | || |||||| || || || ||||||| || ||||||||||| || |||||||| |||||||| ||||| | ||| |||||||| ||||||||||| |||||||||
gtaagtggaatgcatgactctcagaattttgcttctgattcatttaaatttctgttatctcaagggtgaaataacagGTCTTGTGCGATAGGCACTTCGGGGGAATTAACTATCCAGTTGGTGGTGTTGGTGGTATTGCTATGTCCTTGGCAGATGGGCTTGTTGACAAAGGCAGTG
upper sequence: AT1G06820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 5
------------------gtaggattcttgtttttgcatttggtgtctactcgtgttaccctttattttattttttcttatg-----tcttcaaggacagGTTTTATGTGACAGGCACTATGGAGGAATTAACTACCCGGTTGGTGGAGTTGGTGGGATTGCCAAGTCTTTGGCAGAAGGGCTTGTTGATCAAGGCAGTG
||| | ||| | || | | | | || | || |||| | | || | ||| |||||| |||||||||| |||| ||| || ||||||||||| |||| || |||||||||||||| ||||| || ||| |||| || |||||||| || ||||
acactaatgtaatgtcaagtatagtgtccatttgcatagttcacctatgcctctcttgctctccatttcctgcatagctagactcctttttctccttcagGTTCTATGTGACAGACACTTTGGTGGGATTAACTACCCTCTTGGGGGTGTTGGTGGGATTGCAAAGTCCTTAGCAAAAGGTCTCGTTGATCAGGGTAGTG
upper sequence: AT1G06820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G34060.1 (Glycine max), 3'ss of exon 5
------------------gtaggattcttgtttttgcatttggtgtctactcgtgttaccctttattttattttt--tcttatgtcttcaagg---acagGTTTTATGTGACAGGCACTATGGAGGAATTAACTACCCGGTTGGTGGAGTTGGTGGGATTGCCAAGTCTTTGGCAGAAGGGCTTGTTGATCAAGGCAGTG
||| | || | || ||| | | || | || |||| | | | | ||| |||||| |||||||||| |||| ||| || ||||||||||| |||| || ||||||||||| || ||||| || ||| |||| || |||||||| || || |
acactaatgtaatgtgaagtatagtgtcctgttgcatagttcacctctgcctctcttgctctccatttcctgcatggcttgacacctttttttcctccagGTTCTATGTGACAGACACTTTGGTGGGATTAACTACCCTCTTGGGGGTGTTGGTGGGATAGCAAAGTCCTTAGCAAAAGGTCTCGTTGATCAGGGTAGCG
upper sequence: AT1G06820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0032g00800.t01 (Vitis vinifera), 3'ss of exon 5
gtaggattcttgtttttgcatttggtgtctactcgtgttaccctttattttattttttcttatgtcttcaaggacagGTTTTATGTGACAGGCACTATGGAGGAATTAACTACCCGGTTGGTGGAGTTGGTGGGATTGCCAAGTCTTTGGCAGAAGGGCTTGTTGATCAAGGCAGTG
||| | || | || | | | |||| | | || | | ||| | |||| | ||||| |||||| ||||||| ||||| | ||| |||||||||||||| |||||||| |||||||| ||||| ||||| |||||| |||| || ||||| | |||||||
gtaagcttttaattgccttttgttctctctatttttatt-tcttagctttcctgaaatcttgtttcttc-----cagGTTCTATGTGATAGGCATTTTGGGGGAATTAACTACCCTGTTGGTGGTGTTGGTGGAATTGCTAAGTCCTTGGCAAAAGGTCTAGTTGAAAATGGCAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgtctactcgtgttaccctttattttattttttcttatgtcttcaaggacagGTTTTATGTGACAGGCACTATGGAGGAATTAACTACCCGGTTGGTGGAGTTGGTGGGATTGCCAAGTCTTTGGCAGAAGGGCTTGTTGATCAAGGCAGTG
ccctttattttatttt CT-rich tract
tttattttattttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggattcttgtttttgcatttggtgtctactcgtgttaccctttattttattttttcttatgtcttcaaggacagGTTTTATGTGACAGGCACTATGGAGGAATTAACTACCCGGTTGGTGGAGTTGGTGGGATTGCCAAGTCTTTGGCAGAAGGGCTTGTTGATCAAGGCAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG