Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcttcttgagtgttttctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 1
---------------------gtgagtcttct-----tgag--tgttttctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
||| | | | |||| | | | | || || | ||| || || |||| | ||||||| |||||| ||||||||||| ||||| ||| | ||||| |||||||| || ||||||| || ||||||||| ||||||||||| | ||||||||||| || ||||
tcccttatctagttcaaggtggtgcatatcatacagatgaggctctacttttggaaatatcatcaatctaatggaatttgc-aatgcttctgttttt---gaagGTTTGTGATGATCGTCATTCAGAGTTGATTCCCTGCTTAGACAGACATCTTATCTATCAAATGAGACTGAAGCTGGATCTTTCTTTGATGGAACACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 2
-------------gtgagtcttcttgagtgttttctcaatgatggttat-------gttca--agtggtat----atgttaatg-tgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
| | ||| || | | ||| ||| |||| ||| | ||| || || | |||| | ||||| | |||| |||||| ||||||||||| ||||| ||| | ||||| ||||||||||| ||||||| || |||||||| |||||||||| ||||| |||||||||| ||||
ataagtagacacaatcaag-ttcatgggcatcatctaaat-atggctatacttttggctcatcagcagtctcatggtgtttacaatgtttatgtttt-tgaagGTCTGTGATGATCGTCATTCAGAGTTGATTCCCTGCTTAGATAGACATCTTATCTATCAAATGAGGATGAAGCTGGACCTGTCTGTGATGGAGCACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 2
----------------------gtgagtctt-cttgagtgttttctcaatgatggttatgttcaagtggtata-tgttaatg-tgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
|| | | | | | | | | ||| | ||| || |||| ||||| | |||| |||||| ||||||||||| ||||| ||| | ||||| ||||||||||| | ||||| || |||||||| |||||||||| ||||| |||||||||| ||||
ataagtgggcacaatcaagttcatgggcatcatctaaatatgactatacttttggctcatcagcagtctcatggtgtttgcaatgtttatgtttt-tgaagGTTTGTGATGATCGTCATTCAGAGTTGATTCCCTGCTTAGATAGACACCTTATCTATCAAATGAGGATGAAGCTGGACCTGTCTGTGATGGAGCACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G34890.2 (Glycine max), 3'ss of exon 2
-----------------------------------------------gtgagtcttcttgagtgttttctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
|| || |||| | | || ||||| | || ||| | | | || ||||| ||||| |||||||||||| || ||||| |||||||| | || || ||||| |||||||||| ||||||||||| ||||| |||||||||||||| ||||
gtgagttaaattaagattttgaaatgaaaaagttttttgttttcccttcatgttagtttctagtttttactacttttgacacccttcaacttgtttatactcttcttttaactttttt--aagGTCTGTGATGATCGATTATCCGAGCTGATTCCTTGTCTGGACAGAAATCTCATATACCAAACAAGATTGAAGCTTGATTTATCTTTGATGGAGCACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 2
----------------------------gtgagtcttcttgagtgttttctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
| | | | | | | || || | ||| || | |||||| | ||||||| |||||| ||||||||||| ||||| || | ||||| |||||||| || ||||||| || ||||||||| ||||| ||||| | ||||||||||| || ||||
tcccctatctagttcaaggtggtgcatatcatataggcaaggctctacttttggaaatatcatcaatctaatgg-attttttaatgcttctgttttt---gaagGTTTGTGATGATCGTCATTCAGAATTGATTCCCTGCTTAGACAGACATCTTATCTATCAAATGAGACTGAAGTTGGATCTTTCTTTGATGGAACACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 1
---------------------------gtgagtcttct-tgagt-----gttttctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
||| || | | ||| |||| | | ||| ||||| | || || | | | || ||||| ||||| |||||||||||| || ||||| |||||||| | || || || || |||||||||| ||||||||||| ||||| |||||||||||||| ||||
gtgagttaaattaagattttgaactgaacaagttttatgttagtttctagtttctactactatgacacccttcaacttgtttaaactcttcttttaactttttt--aagGTCTGTGATGATCGATTATCCGAGCTGATTCCTTGTCTGGACAGAAACCTCATATACCAAACAAGATTGAAGCTTGATTTATCTTTGATGGAGCACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 1
------------------------gtgagtcttc--ttgagtgttttc-----tcaatgatggttatgttcaa---gtggtatatgttaatgtg--tttgtttt----ttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
| | || || | ||| | || ||| | |||| | | || ||| |||| | | ||| || || ||||| ||||||||||| | |||||||| ||||| || |||| || ||| | |||||||||| ||||||||||| ||| || | ||||||||||| ||||
gtgagttatcttagtctgaactgaacaacttttacatttatcctttccaataaccatgaatgttaatgtctagtgtgaggcataagttattttaatcttgcattcaatttgttaagGTCTGTGATGATCGTCTCTCGGAGCTAATTCCATGTCTAGACAGAAATTTCATATACCAAACAAGATTGAAGCTTGATCTGACGTTGATGGAGCACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G04370.1 (Glycine max), 3'ss of exon 1
---------------------------------------------gtgagtcttcttgagtgttt-tctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
| | ||||| |||| | || | ||| | || ||| | | | | ||| || ||||||| |||| ||||||||||| | |||||||| ||||| || |||| || ||| | |||||||||| ||||||||||| ||| || |||| |||||||| || |
gtgagttatcttagtctgaactgaacaacttatacatttaccctttccaatagccttgaatgttggtgtctagtatgagt-cattatagttattt-tactcttgtattcatttttta---agGTCTGTGATGATCGTCTATCGGAGCTGATTCCATGTCTAGACAGAAATTTCATATACCAAACAAGATTGAAGCTTGATCTGACTTTAATGGAGCACTACG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------gtgagtcttcttgagtgttttctcaatgatggttatgttcaagtggtatatgttaatg------tgtttgttttt-----tacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
| | | |||| | ||| | || | |||| |||| | | | || ||| ||||| | || | |||||| ||||||||||| ||||| || | ||||| ||| ||||||||||||||||||||||||||||||||||||||||| | |||||||||||||| ||||
gtaagtttctagtagctgagctggaatcagcaccagtactagcctcctcttctctttgacactttgacttgtttatttttgcttcttatattcagttttcttttattgatggtgtcatgtttctgcttctgattttgaagGTTTGTGATGATCGGCATTCTGAATTAATTCCCTGCCTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATCTTTCTTTGATGGAGCACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------gtgagtcttcttgagtgttttctcaatg-atggttatgttcaagtggtatatgttaat-gtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
||| | | | | || ||| | | | |||| | | | ||| || | | |||| |||| |||||| |||||||||| ||||| ||| | ||||||||| |||| ||| | |||||||| ||| | |||||| |||||||||||||||||||||| ||||
gtgagttgtttccagctgaacaacttttacctctctacctagtgaattgaattagtgtcattcttagctctgtatgtcctggtgtttgactaatttatctttcttatatttgcctttt--gaagGTTTGTGATGATCACCATTCAGAGTTGATTCCTTGCCTAGACAGGCACTTTATATACAAAACAAAGTTGAAGTTGGATTTGTCTTTGATGGAGCACTATG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S322_38V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------gtgagtcttcttgagtgtt----ttctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
|| | | || || ||| | || | || | || || | | | || | || | | |||| |||||| ||||| | ||| | |||||||| | |||||| |||| | | |||||| | |||||||| ||||||| ||||||||||||||||
tctaaggtattgttctatttgtaattggtccgaagggttcgtgtcctttaggacgtgtaaattacctttgaagatccgacactgagacaagagtctgcagGTCTGTGATCATCGATTCACAGAGTTGGTTCCTTGCCTGGATAGGGATCTGAACCATAAAATGAAACTGAAGCTGAATTTGTCGTTGATGGAGCATTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
tgttaat putative branch site (score: 3)
tttgtttttt putative PPT
tatatgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcttcttgagtgttttctcaatgatggttatgttcaagtggtatatgttaatgtgtttgttttttacgaagGTGTGTGATGATCGACATTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATTTGTCTTTGATGGAGCATTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA