Sequence
atgc intronic sequence ATGC exonic sequencegttttgtgtttctccgtctctctctctttctctgtgtctgtatttcctctttgtcattataatcatgaaactgttatcggtttcgtagcagAGCTGGAGACGATGAAGGAAAGATTCTCGAAGCTTCTGCTTGGGGAAGATATGTCAGGAAGCGGCAAAGGCGTTTGCACCGCAGTGACAATCTCAAACGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01700.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G39560.1 (Glycine max), 3'ss of exon 2
gttttgtgtttctccgtctctctctctttctctgtgtctgtatttcctctttgtcattataatcatgaaactgttatcggtttcgtagcagAGCTGGAGACGATGAAGGAAAGATTCTCGAAGCTTCTGCTTGGGGAAGATATGTCAGGAAGCGGCAAAGGCGTTTGCACCGCAGTGACAATCTCAAACGC
||| | ||| || | || || | | || | || || | | | || || | |||| ||||| || ||||||||||||||| | ||||||||||| || ||||| ||||| ||||| || ||||| |||||||| ||||| |||||||||||
gttatttgtgaa---gttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacattatagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
upper sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G46690.1 (Glycine max), 3'ss of exon 1
--------------------gttt-tgtgtttctccgtctctctctctttctctgt---gtctgtat--ttcctctttgtcattataatcatgaaactgttatcggtttcgtagcagAGCTGGAGACGATGAAGGAAAGATTCTCGAAGCTTCTGCTTGGGGAAGATATGTCAGGAAGCGGCAAAGGCGTTTGCACCGCAGTGACAATCTCAAACGC
|||| |||| || | || | | | || | || || || || | || | | | | | || || | |||| ||||| || |||||||||||||| | ||||||||||| || ||||| ||||| ||||| || ||||| |||||||| ||||| |||||||||||
gttggtttgcactttgcatagtttgtgtggttatttgtgaagttttaggacactttgaagtttgaatgattacaaatttcagtagtggttgacttaattttgtccacattatagCCGAGCTTGAATTAATGAAGGAAAGATTTGCAAAGCTTCTGCTGGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
upper sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g02530.t01 (Vitis vinifera), 3'ss of exon 1
gttttgtgtttctccgtctctctctctttctctgtgtctgtatttcctctttgtcattataatcatgaaactgttatcgg--tttcgtagcagAGCTGGAGACGATGAAGGAAAGATTCTCGAAGCTTCTGCTTGGGGAAGATATGTCAGGAAGCGGCAAAGGCGTTTGCACCGCAGTGACAATCTCAAACGC
| ||| ||| || | | | || || | | | | | | |||| ||| | |||| |||||||| || ||||||||||||||| || |||||| |||| || ||||| ||||||||||||||||||||||| ||||| || || ||||||||||| ||
-----------gtgggtccaaacctcatttccggggaagctaaggtctggattctaatctgcttaactaacttgtatttgattttctgggcagAGCTTGAACTGATGAAGGAAAGATTTTCCAAGCTTTTGCTGGGTGAAGACATGTCAGGAAGCGGCAAAGGCGTCTGCACTGCGGTCACAATCTCAAATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtatttcctctttgtcattataatcatgaaactgttatcggtttcgtagcagAGCTGGAGACGATGAAGGAAAGATTCTCGAAGCTTCTGCTTGGGGAAGATATGTCAGGAAGCGGCAAAGGCGTTTGCACCGCAGTGACAATCTCAAACGC
attataatcatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgtgtttctccgtctctctctctttctctgtgtctgtatttcctctttgtcattataatcatgaaactgttatcggtttcgtagcagAGCTGGAGACGATGAAGGAAAGATTCTCGAAGCTTCTGCTTGGGGAAGATATGTCAGGAAGCGGCAAAGGCGTTTGCACCGCAGTGACAATCTCAAACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG