Sequence
atgc intronic sequence ATGC exonic sequencegtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacctcaaaatatttttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03190.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 5
gtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacctcaaaatatttttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
| ||| | ||| | ||||||| | || || |||| || || | | |||||| || | | || ||| | ||| |||| |||| || ||||| || ||| | || ||||||||||||| ||||||||| || ||||||||||| || |||||||| | | ||| || ||||| |||||||
-----------------------------------tgcttttactgttct-catgaat-acagcattcttgg-----caaagccttgataac-acgcaatgcattagcaccta---atatgaaaatcttatgacttca------atttgcagGACATCATGCAGCATAAGTTGGTATTCATTGAAACACCAGATGTTGTTGAGACAACATTGGCTCTTGATAATTACAGAAAGGCATGTGATTGTGGAAGAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 6
gtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacctcaaaatatttttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
| | || || | ||| |||| | || | ||| | || || | |||| |||| || | | || | | | ||| |||||||||||||||| || ||||| || ||||| || || ||||| ||||| || |||||||| || ||||| ||||||| |||||| ||||| |||||||
----------------------------------------------------gttagttagattcttt--gatatc-cagtccacgggtaga-gtagtagtatttgttatata---gtttggtggtgtgctaaaagcatcttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 6
gtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacc-tcaaaatatt--tttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
| | | || || | || | || | || | || | || ||| | | ||| | || || || || || | || | | || | ||| |||||||||||||||| || ||||| || ||||| || || ||||| ||||| || |||||||| || ||||| || |||| |||||| ||||| |||||||
--------------------------------------------gtgaggggactagttagattcttcaatatccagtccatttactggttgagtagtagtatctgtta-tatagtttggtggtgtgctaaaagcatctttgtttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 6
gtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacctcaaaatatttttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
| | | | |||| | || | ||| || || ||||||| || | | | |||| ||| || | |||| | ||| || | |||| | |||||||||||||||| |||||||| || ||||| || || ||||| || ||||| ||||| || || || ||||||||||| ||||| || || || ||||
---------------------------------accgtctgtatagttctacacacac-----tttccctgg------gaattatttttgctttatagaaaaactaat-----tttcttgatagatact--taatgctatctttgtt-gcagGAAATAATGCAACATAAGCTTGTCTTTATTGAGACTCAGGATGTGGTGGAAACTACATTAGCTCTAGACAATTATCGCAGAGCTTGTGACTGTGGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
attaatgtatatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacctcaaaatatttttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA