Sequence
atgc intronic sequence ATGC exonic sequencegttagctgaggttttaactgcataaggtcaaagttccgctctttatgtaattgatatcataattgttttgacatgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G28030.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G28030.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g10780.1 (Oryza sativa), 3'ss of exon 9
-----------gttagctgaggtt-ttaactgcataaggtcaaagttccgctc---tttatgtaattgatatcataattgttt------tgac-atgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
| | || | || ||| | | || ||| | || | ||| ||| | | || || ||| ||| ||||||||| ||||| ||||| |||||||||||||||| || ||||| ||||| |||||||| || || || | || |||||||||||||| ||||||||
actttaattatgccatctcaatttcttattttgaaggggggaaaatgccatttcagtttctgttttgtccagtgtatttatttatatactgattatgcagTGGCATTGGCATTGTGAATGCTATTGAAGTTGCACACGCATTTCCTGAGGAAGATGGGCTCCAAAAGTTCAGGGAGTGGGTTGAATCACCAGATCCAACT
upper sequence: AT3G28030.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G388915_T01 (Zea mays), 3'ss of exon 10
---------------gttagctgaggttttaactgcataaggtcaa---agttccgctctttatgtaattgatatcataatt----gttttgacatgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
| | | | | ||| | | | | || | | || || | || | | ||| | || ||||||||||| || || || ||||||||||||||||| ||| ||||| || || ||||| || ||||| ||| |||||| |||||||||| |||||| |
agtattctaaagtgcagcaccaaaatgcaacattccatccgatgcatttatttttgttggttttgcgctaaatttttttattttatatgctggtgtgcagTGGTATCGGCATCGTGAATGCTATTGAAGTTGTACATGCATTTCCTGAAGAAGATGGACTGCAGAAGTTTAAAGAATGGATTGAATCACCAGATCCATCA
upper sequence: AT3G28030.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 13
----------------gttagctgaggttttaactgcataaggtcaaagttccgctctttatgtaattgatatcataatt--gttttga-----catgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
| | | ||| | || | | | |||| || | |||| | |||| || || || ||| ||| ||||| ||||| ||||| ||||||||||| ||||||| ||| || || ||||| ||||| || | |||||| || |||||||||| ||||| ||||| |||
ctttccttgtatttctttgtagtaggatttctgtggtattatatataggttctgca-tctatgaacttgactagatccttttgtgttgcatgctaatgtagTGGGATTGGCATTGTTAATGCTATTGAGGTTGTGAATGCATTCCCTGAGGAAGATGGCCTCCTGAAATTCCGGCAATGGGTTGAGTCACCGGATCCCACC
upper sequence: AT3G28030.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv14s0066g01630.t01 (Vitis vinifera), 3'ss of exon 10
----------------------gttagctgaggttttaactgcataaggtcaaagttccgctctttatgtaattgatatcataattgttttgac-atgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
|| | || | || | | ||| |||| ||| | | ||| ||| | | ||| | ||| ||||| ||||| ||||| ||||||||||||||| | | | ||||||| |||||||| || ||||| || || || || |||||||||||||| ||||||| |
tttatcagtagatacacaggatgtatacacagatgttgagttcatgtttattaagtaaatatctaatttttatttttattttt-tggttcaaatgatgtagTGGAATTGGCATTGTTAATGCTATTGAAGTTTTAAATTCTTTTCCTGAGGAGGACGGTCTTCATAAGTTCCGGGAGTGGGTTGAATCACCAGATCCAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggtcaaagttccgctctttatgtaattgatatcataattgttttgacatgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
ttttgac putative branch site (score: 3)
ttgtttt CT-rich tract
tttatgtaattgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctgaggttttaactgcataaggtcaaagttccgctctttatgtaattgatatcataattgttttgacatgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG