Sequence
atgc intronic sequence ATGC exonic sequence...ctggttgaaattgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01790.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 8
ctggttgaaattgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctctttt-cagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
| || || || | | | | | || | | | | | | | || | |||| || |||| || ||||| || || ||||| | || | |||||||||||||||| || ||||| ||||| ||||||||||| || |||||
ccatgggacgccgc-aacgcctcaaaaaccatgcccagtttacacctccttttgatctgtttgatccttgagacctttgtgcaatacgtgtttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 9
ctggttgaaattgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtt---tctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
|| | ||| | | ||| | | | || | || | | | | ||||| | || ||| | | | | ||| || |||| || ||||| || || ||||| | || | |||||||||||||||| || ||||| ||||| ||||||||||| || |||||
ttgccataggatgccgcaacgcctcaaaaacc---attcccagtttacacctccttaactgtttggtccttgaggccttcgttcaatatctggttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 16
-----ctggttgaaattgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
|||||| |||| | | | | | | ||||||| | || | | | | || || | | | | ||||||| |||| |||||||| ||||||||||| ||||| || ||||| || || |||||||| || || ||||| ||||||||||| || || |
cttctgtggttgtcattgttattttttc-----tacatgtatactctgctattgcttctttgttgtcctcaactcctcattagaaataccaatctatattttcagGTTGGTTTTCAAGCTATTGCTGAAGCACTTGGACTGGCTGCTGTTAAGGCAGCAGTTGCCATCACTGCCATAATTGCTGGGGGACGATTG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 12
ctggttgaaattgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaat--gctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
| ||| | | | | |||| | | || | | ||| ||| | | || || | | | | | | | | | | ||||||| |||| |||||||| ||||||||||| ||||| || ||||| || || |||||||| || || ||||| |||||||| || || ||| |
taaatcaaaaaggtcaagacacga-atatctttctaaa-taaagttggtccatgtaagcgcatgattggtagtgttgacataataccaatctatattttcagGTTGGTTTTCAAGCTATTGCTGAAGCACTTGGACTGGCTGCTGTTAAGGCAGCAGTTGCCATCACTGCTATAATTGCAGGGGGACGTTTG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 8
ctggttgaa--attgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
| ||| || ||| | | |||| | ||| |||| | |||| || | | ||| || | | | | | ||||||| |||| || ||||||||||||||||||||||| || ||||| || || |||| || || ||| | || |||||||||||||| || |
catgttaaatgcttgactggaagccaatgacttcaccttacttttgtcagtcattatcatctatcttgtctttttgtgt--aataccaatctcagttttcagGTTGGTTTCCAAGCCATTGCTGAAGCTCTTGGTCTGGCTGCTGTTAAGGCAGTGGTTGCCATTTCAGCCATAATTGCTGGTGGACGATTG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G01600.1 (Glycine max), 3'ss of exon 2
ctggttgaaa--ttgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
||| || ||| | | | |||| | ||| |||| | | | | ||| || | | || || | | | || ||| ||| |||| || ||||||||||||||||||||||| || ||||| ||||| |||| || |||||| | || |||||||| ||||| || |
--tgttaaatgcttgattgaaagccaatgacttcaccttacttctctcattgtcatcatcatctatgttgtctttttgtgaaataccaatctctgtttccagGTTGGTTTCCAAGCCATTGCTGAAGCTCTTGGTCTGGCTGCTGTCAAGGCAGTGGTTGCTATTTCAGCCATAATTGCAGGTGGACGATTG
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 7
ctggttgaaattgctggt-atgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaat-gctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
| | | || | |||| | || | | ||| | | || | | | | | | | || |||||||||||| ||||||||||||||||||||||| || || ||||| || || ||| ||| || ||| |||| |||||||||||||| || |
--ttctccatgcgttgatcatgcttctttgttgtcagttgtcactactattactgctgcttctattcttatgttgttatcatggcaacaattctgttttcagATTGGTTTTCAAGCCATTGCTGAAGCTCTCGGACTGGCTGCTGTTAAGGCATTAGTTGCCATTGCTGCCATAATTGCTGGTGGACGCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
tttctactgctctttt CT-rich tract
aaatatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggttgaaattgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctcttttcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - caaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcaaaa