Sequence
atgc intronic sequence ATGC exonic sequencegttagaagtcagtcatttgttttctactatttatattttaactgtttattaacttttttctccattttcaatcaatactcagAATTCAAGTTAGTCACCAGAGAAATCTGCAAGCTCCCATCTTTCTTCTCCACTTCCCTTTTCCGGAAGATCGATCTCAACAATACAGGTTTTGTTACTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28850.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 3
----------gttagaagtcagtcatttgttttctactat-ttata---ttttaactgtttatt-----aacttttttctccattttcaatcaatactcagAATTCAAGTTAGTCACCAGAGAAATCTGCAAGCTCCCATCTTTCTTCTCCACTTCCCTTTTCCGGAAGATCGATCTCAACAATACAGGTTTTGTTACTAG
| | | |||| ||| || ||| ||| | || |||| | || || |||| ||||| ||| ||||||||||| | | | || | ||| | |||||||| |||||||| || |||||||||||||||| |||||| || ||| || ||| |||| || ||
atattgcctcatgatctttataacattcactttttaatatattaaagagttgtaacagcgagttctgagaatcattttacttgttttcttggaatg-tcagAATTCAAATCAATTACTAAGGAAGTTTGCAAGCTGCCATCTTTTTTTTCCACTTCCCTTTTCCAGAAGATTGA---CAATGGAACTGGTGTTGTGACAAG
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G30930.2 (Glycine max), 3'ss of exon 3
--gttagaagtcagtc--------atttgttttctactat-ttata---ttttaactgtttatt----aacttttttctccattttcaatcaatactcagAATTCAAGTTAGTCACCAGAGAAATCTGCAAGCTCCCATCTTTCTTCTCCACTTCCCTTTTCCGGAAGATCGATCTCAACAATACAGGTTTTGTTACTAG
|| | || || || ||| || ||| ||| | || |||| | ||| | | ||| | |||| || | ||||||||||| | | | || | ||| | |||||||| |||||||| || |||||||||||||||| ||||| || ||| || ||| |||| || ||
atattgtctgacaatctttataaaatacactttttaatatattaaagagttgtaacagccaattctgagaatcattttactttttttcttcgaatgtcagAATTCAAATCAATTACTAAGGAAGTTTGCAAGCTGCCATCTTTTTTTTCCACTTCCCTTTTCCAAAAGATTGA---CAATGGAACTGGTGTTGTGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttatattttaactgtttattaacttttttctccattttcaatcaatactcagAATTCAAGTTAGTCACCAGAGAAATCTGCAAGCTCCCATCTTTCTTCTCCACTTCCCTTTTCCGGAAGATCGATCTCAACAATACAGGTTTTGTTACTAG
tattaac putative branch site (score: 1)
cttttttctccatttt CT-rich tract
atattttaactgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaagtcagtcatttgttttctactatttatattttaactgtttattaacttttttctccattttcaatcaatactcagAATTCAAGTTAGTCACCAGAGAAATCTGCAAGCTCCCATCTTTCTTCTCCACTTCCCTTTTCCGGAAGATCGATCTCAACAATACAGGTTTTGTTACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA