Sequence
atgc intronic sequence ATGC exonic sequencegcatggttcctctttatatttttctgctattccatctctgatatgcgattggcattctactagaaaattatattgaaactgactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G22770.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
gcatggttcctctttatatttttctgctattccatctctgatatgcgattggcattctactagaaaattatattgaaactgactcatttcatctca-acagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
|| ||| ||| | | || | | || || | || ||| | || ||| || | | ||| || | || | || | |||||||||||| | ||||| || ||||| |||||||| ||||| ||||| || ||||| |||||||||||||| || |||||||||||||| || |
-caaagttggaatttgattatgtcgtaaaatatatgcaccctacatgttttagcttcatattgacttatattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 10
gcatggttcctctttatatttttctgctattccatctctgatatgcgattggcattctactagaa--aattatattgaaactgactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
| | | | | || || | |||| | || | |||| | | | || || || | | | | | | || | |||||||||||| | || || || || || |||||||| ||||| ||||| || || | ||||||||||| ||||| |||||||||||||| || |
atgttataacaaacgaaagttggaaattagcttccccttgatttattgctgac-ttctgtttgcattgatcattttcctgtctgcacctgac-taccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGGCCTGATGTTGAGTGGAGAATATGTA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G107101_T01 (Zea mays), 3'ss of exon 11
gcatggttcctctttatatttttctgctattccatctctgatatgcgattggcattctactagaa-aattatattgaaactgactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
| | | | | | || ||| || | ||| | | | | | || || || | || | | || | |||||||||||| | || || || || || |||||||| ||||| ||||| || || | ||||||||||| ||||| |||||||||||||| || |
-tgttataacaacccaaagtaggaaattagcttccttctaatttattgttgacttctttttgcattgatcatttttctgtctgaaccttaactaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGCCCTGATGTTGAGTGGAGAATATGTA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 4
-------gcatggtt-cctctttatatttttctgctattccatctctgatatgcgattggcattctactagaaaatt---ata---ttgaaa-ctgactcatttcatctcaa-cagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
||| || | || | |||||| | | ||| || | | | || || |||| || ||| |||||| || | | ||| | | | |||||||||||||||||||| ||||| | |||||||| ||||||||||| ||||| |||||||||||||| |||||||| || ||||| |||||||||||||
gttgtgtgcaactttatcagttaacatttttttttcttgattattcttattttttacagtcactcacgtagattctttccatacacttgaaatctaaaacctttgttgttgatcagATAGAAGTTCCTGCAGCTGAAGCCTCAATTGAAGCTACTGCCCAAGGCATTGCATCAATGCTTTGTGCCCATGGTCCAGAGGTTGAATGGAGAATTTGCA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G36600.2 (Glycine max), 3'ss of exon 10
-------------gcat-ggttcctctttatatttttctgctattccatctctgatatgcgattggcattctactagaaaatt-----ata-ttgaaa-ctgactcatttcatctcaa-cagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
|| ||| ||| |||||| | ||| || | || || | | || || |||| || | | |||| | || | ||||| | | | |||||||||||||||||||| ||||| | |||||||| ||||||||||| ||||| |||||||||||||| |||||||| || ||||| |||||||||||||
gttgtgttcacctttatcagttaacatttttattttctt--tatgttattcttaatttgt-acagtcactcatgtagattctttccgtacacttgagatctaaaacatttgttgttgatcagATAGAAGTTCCTGCAGCTGAAGCCTCTATTGAAGCTACTGCCCAAGGCATTGCATCAATGCTTTGTGCCCATGGTCCAGAGGTTGAATGGAGAATTTGCA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G07240.2 (Glycine max), 3'ss of exon 10
gcatggttcctctttatat-ttttctgctattccatctctgatatgcgattggcattctactagaaaat-tatattgaaact----gactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
| |||| |||||| | || || | || | | | |||| | || ||| | || || |||| | | || | | ||||| |||| | || |||| ||||| || |||||||| || |||||||| ||||||||| ||||||| ||||||||||| || || |||||||||||||| |
gttcggttactctttgcaagttacctcatttttctcattttgtatggtaatgtagagctaattctttatgcatgctgaagatctataatatatatttgtctatcagATTGAAGCTGCTTCAGCCGAAGCCACTATTGAAGCTACGGCCCAAGGCATTGCCTCAGTGCTTTGCGCTCATGGTCCAGAGGTAGAGTGGAGAATTTGTA
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------------------------------------------gcatggttcctctttatatttttctgctattccatctctgatatgc-----gattggcattctactaga----------aaattatattgaaactgactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
|||| || | ||| | || | || | | | | | | ||| || | | | | || || |||||| | | | | ||| ||||||||||| |||||| | |||||||| |||||||||||||||||||| ||||| |||||||||||||| |||||||| || ||||| |||||||||||||
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgattggcattctactagaaaattatattgaaactgactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
aactgac putative branch site (score: 2)
tttcatctc putative PPT
attctactagaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatggttcctctttatatttttctgctattccatctctgatatgcgattggcattctactagaaaattatattgaaactgactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA