Sequence
atgc intronic sequence ATGC exonic sequencegttagtctctcttcaactactcaagttctctaatcagttctgatcggtcgaggttataattttccgtggtttctttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31850.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G34640.1 (Glycine max), 3'ss of exon 3
-------------------gttagtctctcttcaactactcaagttctctaatcagttctgatcggtcgaggtta---taattttccgtggtttctttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
| | | || || | | | | | || || || ||| | || || || ||| || |||||||| |||||||| || || | ||||| |||||||| ||| || | |||||||| ||||||||||||||||||||||| |||||||||||||| || |
acttatttaaatactaataatgaatttcagtt-actaatttcaatcaagatatagacaaggagtggcatcaattaatccacttaaccctgatttgtt--atagGTTGCTAGCTGGGGTGGTGACTTGTTGGATCGTGGGATTCTAACAATTTCTCTTGCCCCAAGAGATAACCATGAAGCTCAAGTTCAATTTGCTCTAGAGC
upper sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G17500.1 (Glycine max), 3'ss of exon 4
--------gttagtctctcttcaactactcaagttct-ctaatcagttctgatcggtcgaggttataattt------tccgtggtttctttgg----tagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
|| || ||| | || |||| | ||||||| || | | | ||| || ||| || || |||||||| |||||||| || || | | || |||||||| ||| | || |||||||| |||||||||||||||||||||||||||||||||||||| || |
aattcctatttcatccttctaattttgatctagttttactaatcaaacatgttatagacaagacatacgttgattaatccacaattctatttcactttagGTTGCTAGCTGGGGTGGTGACTTGCTAGATCGTGGGATTCTAACTCTTTCTCTTGCACCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTGGAGC
upper sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G35220.5 (Glycine max), 3'ss of exon 4
gttagtctctcttca-actactcaagttctctaatcagttctgatcggtcgagg--------------ttataattttccgtggtt----tctttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
||| | | | |||| | || ||| | | | || |||| | || || | | | | | | | | |||||||| |||||||| || || | ||||| || ||||| ||| || | |||||||| ||||||||||||||||||||||| |||||||||||||| || |
gttcactcatttaaatactaattaatttcagttacaaatttcgatcaggtgatagacaaggagtgcatcaattaatccacttaactctgatttgttatagGTTGCTAGCTGGGGTGGTGACTTGTTGGATCGCGGGATTCTAACAGTTTCTCTTGCCCCAAGAGATAACCATGAAGCTCAAGTTCAATTTGCTCTAGAGC
upper sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G08120.1 (Glycine max), 3'ss of exon 4
-----------gttagtctctcttcaactactcaagttct-ctaatcagttctgat-cggtcgaggtt---ataattt--tccgtg-gtttctttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
|| | |||| || | ||| || |||||| || | | | || | || | || ||| | | |||||||| |||||||| || || | |||| |||||||| ||| | || |||||||| ||||||||||||||| ||||||||||||||||||||| || |
tatatttcctatttcttgactctaattctgaaccagtcctattaatcaaacatgttatagacaagactcacatcaattaatccacatacctgtacattagGTTGCTAGCTGGGGTGGTGACTTGCTGGATCGTGGGATTCTAGCTCTGTCTCTTGCACCAAGAGATAACCATCGAGCTCAGGTTCAATTTGCTCTAGAGC
upper sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0033g01120.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------------------------gttagtctctcttcaactactcaagttctctaatcagttctgatcggtcgaggttataattttccgtggtttctttggt---agGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
| || | | | || | || |||| | | | | | | | | || || |||| | ||||||||||||||||||| ||| | || || ||||| |||||| || | ||| | |||||||||||||| ||||| ||||| || |||||||| | ||||
gtgagccctgattcatactattgtttcttcacggagttgatcatatgaaccaattcgataacctattaatctatttgatgtttattctggaagctttgatttatgaccatcacctttgtatatgttcccaaaaattgtgtcacttagtctgtgtaattgctttatttctagGTTGCGAGCTGGGGAGGTGATTTATTAGATCGTGGCATACTAACAATGTCTTTGGCTCCAAGAGATAATCATGAGGCTCAAGTCCAATTTGCATTGGAAC
upper sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S43_170V6.4 (Physcomitrella patens), 3'ss of exon 4
-------------gttagtctctcttcaactactcaagttctctaat----cagttctgatcggtcgaggttataatttt-ccgtggtttct-ttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
|||| | | || || | | ||| || | | | || || |||| | ||| ||| | || |||| || || |||||||| || ||| || | | || || | | | ||||||||||| ||||||| |||||||||||||| ||||| ||| | || |
gattttacgtaatcatagtatataaacagttaggagcatattggaatggaacaaatgtttatgttccagagggtaatgatgttgtgatttttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCTCTTGCTCCTCGAGATAATCATGAAGCTCAGGTGCAATTCGCTTTGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctaatcagttctgatcggtcgaggttataattttccgtggtttctttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
ttctgat putative branch site (score: 3)
tttcttt putative PPT
ttataatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtctctcttcaactactcaagttctctaatcagttctgatcggtcgaggttataattttccgtggtttctttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA