Sequence
atgc intronic sequence ATGC exonic sequencegtgagaatggtgaatgttttcatacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54450.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
-----------gtgagaatggtgaatgttttcatacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
| || | || | || | |||| || ||| || || |||||| || || | || | || | ||||| |||||||||||||||||||||||||| |||||||||| |||| ||||| || |||||||| ||||| |||||||| | ||| ||||||| |||||||| |||
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttg-atctttgtggttgactattagctat-ttgtgat-ttgacgtgtcatgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
--------gtgagaatggtgaatgtttt--catacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
| || | || | |||| ||| | | | ||| | | |||||| || || | || |||| | ||||| |||||||||||||||||||||||||| |||||||||| |||| ||||| || |||||||| ||||| |||||||| | ||| ||||||| |||||||| |||
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctat-ttgtgat-ttgatgtgtcatgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
--------gtgagaatggtgaatgtttt-catacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
| || ||| || ||| ||| | || | || | | | | ||| | | | || || ||| | || | | | || ||||||||||||||| |||||||||| |||||||||| | || |||| || |||||||| ||||| |||||||| | ||| | |||||||||||||| |||
atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaag-tacgagctgacttgaaaatgtcactat-tagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
--------gtgagaatggtgaatgtttt-catacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
| || ||| || ||| ||| | || | || | | | ||| | || | || || ||| | || | | | || ||||||||||||||| |||||||||| |||||||||| |||| |||| || |||||||| ||||| ||||| || | ||| | ||||| |||||||| |||
atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaaag-tacgagctgacttgaaaatgtcactat-tagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
tatattctgttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaatggtgaatgttttcatacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT