Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctggaatagcttttgagttgtcctctatgtttataagctattgttgtgtgtaaacctttgttatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G03650.1 (Glycine max), 3'ss of exon 3
-----gtaagtctgg---aatagcttttgagttgt-----cctctatgtttataagctattgttgtgtgtaaacctttgt-tatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG
|| ||| | || || | | || || ||| || ||| | ||| | |||| ||||| ||| | | |||||||| ||||| || || |||||||| ||||||||||| || || ||| | ||||||||||| || | |||||||||||||||| | ||||||||
gtactatattcatggtctagcaggcattcactggtaaacatgtcaatgcttgaaaggttttgatcacagtaa---tttgtgtatcttttcagATTGGCTTATCTTCATGAAGGTCTTGAACCAAAAGTTGTCCACCGAGATGTGAAATCAAGCAACATACTGATTGATCGCCAATGGAACCCAAAGGTTTCT
upper sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 3
----gtaagtctggaatagcttt-tgagttgtcctctatgtttataagctattgttgtg-----tgtaaacctttgttatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG-
||| | || | ||| | || |||||| | || |||||| || |||| || || | | | |||||||| ||||| || ||||||||||| ||||||||||| || || ||| | |||||||| || || | |||||||||||||||| | ||||||||
taccgtatttgtgattaatcttcatacagtggaatctatgatgatgcttgattgttttgatcactgtactttttgtttgtcttttcagaTTGGCCTATCTTCATGAGGGTCTTGAACCAAAAGTTGTCCACCGAGATGTGAAATCAAGTAACATACTCATTGATCGCCAATGGAACTCCAAGGTTTCTG
upper sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 3
-----gtaagtctggaatagcttt-tgagttgtcctctatgtttataagctattgttgtg-----tgtaaacctttgttatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG
||| | || | ||| | || ||| || | || |||||| || ||| || |||| | | |||||||| ||||| || ||||||||||| || |||||||| || || ||| | |||||||| || || | |||||||||||||||| | ||||||||
gtaccgtatttgtgattaatcttcatacattaaaatctctgatgatgcttgattgttttgataactgtgctttttgtttatcttttcagATTGGCCTATCTTCATGAGGGTCTTGAACCGAAAGTTGTCCACCGAGATGTGAAATCAAGTAACATACTTATTGATCGCCAATGGAACTCCAAGGTTTCC
upper sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G07250.1 (Glycine max), 3'ss of exon 4
-----gtaagtctggaatagcttttgagttgtcctctatgtttataagct---attgttgtgtgta----aacctttgt-tatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG
|| || |||| | | | || | | | ||| |||||| || | ||||| ||| | | |||||||| ||||| || || |||||||| ||||||||||| || || ||| | ||||||||||| || | |||||||||| ||||| | ||||||||
gtactatattcatgatctagcatgcatacactggtatacatgtcaatgcttgaattgttttgatcacagtggtttttgtgtatcttttcagATTGGCTTATCTTCATGAAGGTCTTGAACCAAAAGTTGTCCACCGAGATGTGAAATCAAGCAACATACTCATTGATCGCCAGTGGAACCCAAAGGTTTCT
upper sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtaagtctggaatagcttttgagttgtcctctatgtttataagctattgttgtgtg-taaacctttgttatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG
| | | |||||| | || | | | || | |||| | | || || | |||||||||||| ||||| || ||||||||||| ||||| ||||| ||||| ||| | ||||| ||||| || ||||||||||||||||||| ||||||| ||
gtacctaccctagtctgatatactgaaaactatccaacttttgcccgaaaacattgcttggcaggttgttctaatgtgctttgctatttttgttgctgtagATTGGCCTATCTTCATGAGGGTCTTGAACCAAAGGTTGTCCATCGAGATGTAAAATCTAGCAACATACTACTTGATCGCCAATGGAACTCTAAGGTGTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtcctctatgtttataagctattgttgtgtgtaaacctttgttatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG
tatgtttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctggaatagcttttgagttgtcctctatgtttataagctattgttgtgtgtaaacctttgttatatctgtagATTGGCGTATCTACACGAGGGTCTTGAGCCAAAAGTTGTTCATCGGGATATTAAATCAAGCAATATCTTACTTGATCGCCAATGGAATGCTAAGGTTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA