Sequence
atgc intronic sequence ATGC exonic sequencegtactcaagagtctatttttatttctaatcatctttatgagctacattatataatagctgctaatatacctgtggcagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
-----------gtactcaagagtctatttttatttctaatcatctttatgagc--tacattatataa---tagctgctaatatacctgtgg------------cagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
| ||| | | | | || || ||| ||| |||| || | ||| || | | |||| | ||| | | ||||| || ||||||||||||||||| ||||| ||||| ||||| || |||||||| |||||||| || ||||| | | ||||| || || ||
gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 15
---------------------------------gtactcaagagtctatttttatttctaatc-atctttatgagctacattatataatagctgctaatatacctgtggc-agGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
| |||| | || ||| |||| | || | | | || | |||| || ||||||| || |||| ||||||||||||||| ||||| ||||| || ||| |||| |||||||| || ||||| ||| | |||||||| || ||
gtattaactcttttcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgatacataatgattatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 15
--------------------------------gtactcaagagtc-tatttttatttctaatc-atctttatgagctacattatataatagctgctaatatacctgtggc-agGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
|| |||| | | || ||| |||| | || | | | | || | |||| || ||||||| || |||| ||||||||||||||| ||||| ||||| || ||| |||| |||||||| || ||||| ||| | |||||||| || ||
gtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatgcataatgattatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------gtactcaagagtctatttttatttctaatcatctttatgagctacattatataatagctgctaatatacc----tgtgg---cagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
|| ||| || | | || ||| | || | || | | | || ||| ||| ||| | | | | ||| |||| || ||||||| |||||||||||| || ||||| ||||| || ||| |||||| |||||| ||| || ||| ||||||||||||||||
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaattt-cttatatgtatatttat-tgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
-----------------------------------------------------------------------------gtactcaagagtctatttttatttctaatcatctttatgagctacattatataatagctgctaatatacc----tgtgg---cagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
|| | | || | | || ||| | || | || | | | || ||| ||| ||| | || | | || |||| || ||||||| |||||||||||| || ||||| ||||| || ||| |||||| |||||| ||| || ||| | ||||||||||||||
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaattt-cttatatgtatatttat-tgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 15
----------------------gtactcaagagtctatttttatttcta------atcatctttatgagctacattatataatagctgctaatatacc---tgtggcagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
|| || | ||| | | ||| | | ||| || ||| | | || | | || ||| ||| ||| |||||||||||||||| |||||||||||| || ||||||||||| || ||| | || || ||||||||||| || | |||||||||| |||||
gtattgtgtattgtccacccttgt-cttgaaagtatttccatatgtgcagatgatatccatttcatggatttc-ttggagcttttttgttaaataaccatatgttccagGTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 15
------------gtactcaagagtctatttttatttcta--atcatctttatgagctacattatataatagctgctaatatacctgtggcagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
| || || | ||||| ||| | || ||| || || | || | || | ||| | || |||| | | ||||||||||| |||| ||| |||||||| || |||||||||||||| ||| |||||| ||||| || ||||| | |||||||||| || ||
gtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagt-catataaattgttaatgtgatgatttcagGTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaatcatctttatgagctacattatataatagctgctaatatacctgtggcagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
tgctaat putative branch site (score: 2)
tacattatataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcaagagtctatttttatttctaatcatctttatgagctacattatataatagctgctaatatacctgtggcagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA