Sequence
atgc intronic sequence ATGC exonic sequencegttagaagccactataaatatgatgcctttcaaatccaagttccataaagtgcttgcatagtttggcattttgtatttcagctgagagaattttttgtcccttcttgcgccagTGGAACAAAACAAGCTGCACATAGACTGAAAATTTTATTCGGATTAGCTGGCCTCAAAGCAGCTGAGCTTCATGGAAACCTAACTCAAGCACAACGTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16630.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G25240.1 (Glycine max), 3'ss of exon 8
---------------gttagaagcc-----actataaatatgatgcct-----ttcaaatccaa-gttccataaagtgcttgcatagtttggcatt-ttgtatttcagctgagagaattttttgtcccttcttgcgc----cagTGGAACAAAACAAGCTGCACATAGACTGAAAATTTTATTCGGATTAGCTGGCCTCAAAGCAGCTGAGCTTCATGGAAACCTAACTCAAGCACAACGTCTT
|| ||| | | | | || | | | || |||| | || | | || | | | || || | || || | | || | | | ||| || | || | |||||||||||| ||||||||||||||| |||| ||| |||| |||||||||||| | ||||| ||||||||||||||||| || |||||||| || || |||
gttttcatttcatcatctacaagtctttttatttcagattttaagtctgctccttcatttgcactgctttatgattattatttcccttctgccactattctactacctctaaccaactgtttaatctatcattttgatgtgcagTGGAACAAAGCAAGCTGCACATAGATTGAAGATTATATTTGGATTAGCTGGCTTAAAAGCTGCTGAGCTTCATGGAAATCTTACTCAAGCCCAGCGCCTT
upper sequence: AT4G16630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 8
gttagaagccactataaatatgatgcctttcaaatccaa-gttccataaagtgcttgcatagtttggcattttg-tatttc-agctgagagaattttttgtcccttcttgcgccagTGGAACAAAACAAGCTGCACATAGACTGAAAATTTTATTCGGATTAGCTGGCCTCAAAGCAGCTGAGCTTCATGGAAACCTAACTCAAGCACAACGTCTT
||| | |||| | |||| | || | | || | | | || || | || || || | || | | | | | || || |||||||||||| |||||||| |||||| |||| ||| |||| |||||||||||| ||||| ||||||||||||||||| || |||||||| || || |||
--------------taagtctgat--ccttcatttgcactgctttatgattattatttcccttctgccactctgctacctctaactaattgtttaatctatcattttgatgtgcagTGGAACAAAGCAAGCTGCGCATAGATTGAAGATTATATTTGGATTAGCTGGCTCAAAAGCTGCTGAGCTTCATGGAAATCTTACTCAAGCCCAGCGCCTT
upper sequence: AT4G16630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G15220.1 (Glycine max), 3'ss of exon 7
---------------gttagaagcc-----actataaatatgatgcct-----ttcaaatccaa-gttccataaagtgcttgcatagtttggcatt-ttgtatttcagctgagagaatttt----ttgtcccttcttgcgc-cagTGGAACAAAACAAGCTGCACATAGACTGAAAATTTTATTCGGATTAGCTGGCCTCAAAGCAGCTGAGCTTCATGGAAACCTAACTCAAGCACAACGTCTT
|| ||| | | | | || | | | || |||| | || | | || | | | || || | || | | | || | || | | | | || | | |||||||||||| ||| ||||| ||||| |||||||| |||| |||||||||||| | ||||| |||||||||||||||| || ||||| || || | |
gttttcatttcatcatctacaagtctttttatttcagattttaagtctgctccttcatttgcactgctttatgattattatttcccttctgccactattctgctacctctaaccaaactgtaaaatctatcattttgatgtgcagTGGAACAAAGCAACCTGCAAATAGATTGAAAATTATATTTGGATTAGCTGGCTTAAAAGCTTCTGAGCTTCATGGAAATCTTACTCAGGCCCAGCAGCGC
upper sequence: AT4G16630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 8
gttagaagccactataaatatgatgcctttcaaatccaagttccataaagtgcttgcatagtttggcattttgtatttcagctgagagaattttttgtcccttcttgcgccagTGGAACAAAACAAGCTGCACATAGACTGAAAATTTTATTCGGATTAGCTGGCCTCAAAGCAGCTGAGCTTCATGGAAACCTAACTCAAGCACAACGTCTT
|| ||| | | | | ||| | | ||| | | || || | | ||| ||| | |||||| | || ||||| || ||| ||||||||| ||||||||||||||||| |||| ||||| || ||||| |||||| | || || ||||||||||||||||| || || |||| || ||||||
----caaagtacttctgtttggttatttatca--ttaatattctgtccttttct-gc-tgatatggattttgggctttcagtgtactga---ttttgcattttgttg--gcagTGGAACCAAACAAGCTGCACATAGGTTGAAGATTTTGTTTGGATTGGCTGGCTTTAAGGCTGCTGAGCTTCATGGAAATCTTACACAAGTCCAGCGTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttggcattttgtatttcagctgagagaattttttgtcccttcttgcgccagTGGAACAAAACAAGCTGCACATAGACTGAAAATTTTATTCGGATTAGCTGGCCTCAAAGCAGCTGAGCTTCATGGAAACCTAACTCAAGCACAACGTCTT
ttttttgtcccttctt CT-rich tract
attttgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaagccactataaatatgatgcctttcaaatccaagttccataaagtgcttgcatagtttggcattttgtatttcagctgagagaattttttgtcccttcttgcgccagTGGAACAAAACAAGCTGCACATAGACTGAAAATTTTATTCGGATTAGCTGGCCTCAAAGCAGCTGAGCTTCATGGAAACCTAACTCAAGCACAACGTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA