Sequence
atgc intronic sequence ATGC exonic sequencegtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G17750.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 2
---------gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattt--tgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttc-ttctatt-tgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
|||| ||| | | | | | || |||| || | | | || | | || | | | || | | || ||| ||| | | | | || | || |||| || | | || ||| || | | ||| ||||||||||| || || || || |||||||| ||| | || |||||||||||||| |||||||||||||| || |||| || |||||||| || ||
gtgctctttttctggtccttaattacttggcatttctttattagttcatttgtattaaaatgatacttggtatcatgcttggtgtttgcgtttgtt---aatttgtttatctctaacgatattttttaactccattatatcctgctgacaatataacagAACTGGTTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAACTCTGTCATTGCTGGACGTTACCATGTCACAGAATATCTGGGTTCAGCAGCATTCAGT
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 2
---------------gtctgttccct--tacaatatcg-tggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttattt-gtttcttctat--ttgtcttctgttgcc---cagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
|| ||| || | | ||| | | || | || | || || || | || | | | | | | || | | | |||| | || ||||| || | ||||| || ||| || || ||| ||||| ||||| || || || ||||||||||| ||| | ||||||||||||||||| ||||| ||||| | ||| || | || ||||| || || |||
gtaatgcatttaaatgtttgtcccatattttaatcttactaaagcataaaaaatgatgtggtgattttcagttatctattgtccttgtgtgcctgtgttcacagtgtggcacttaaacctttttataaagtattttgtgtattctaacattatctcctattaattatcagAACTGGCTTTGAAGAAGACAAAAACTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGTTCAGCTGCATTCAGC
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
||| |||| | || | | | | | | | |||| ||| ||| || | || || | || | | | | || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| | ||||| || || |||||||||||| |||| ||||| || || ||||||
-------------------------------------------tgtag-gtactattgttatgttgcaaagtcagtattcttgtcattggtct-gtgttccttttggcc-ttgacatgctatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 2
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
||| |||| | || | | | | | | |||| ||| ||| || | || || | || | | | || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| | ||||| || || |||||||| ||| |||| |||||||| || ||||||
-------------------------------------------tgtag-gtactattgttatgttggaaagtctgtattcttgtcattggtct-gtgttccttttggcc-ttgacatgccatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 2
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
||| ||| || || |||| || | | | |||||| | | | | | | || | |||||| | || || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| || ||||| | || ||||| ||||| || | ||||| || || ||||||
-----------------------------------------gattttttgt---tatgttgtaaagtatgatt-tcttgtctgtttctatgttctcccttttttaacctttatactc-tttcttaaacttagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 4
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
| ||| |||| |||| ||| || | || ||| | | | |||| | || | |||| | | | ||||| | | || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| || ||||| | || ||||| |||||| || | ||||| || || ||||||
--------------------attttttgctatgctgtaaagtatgatttcttgactgtttctatg---------------ttctccc---tttttttaacctttatag--------tccttcttaaactaagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
| | || |||| || | | || | | ||| ||| || | | ||| || || |||| | || ||| | ||| ||||| ||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| || || ||||| || ||| ||||||| ||||| || || |||
--------------------------------------gccagtttcaagttcacaacttttccaccagttttg------ccattgggaactttgcttgttctaacaggaa--gtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
tttatttgtttcttct CT-rich tract
aaatttatttgtttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT