Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacttaaagatgtttgtgtattatgcagattattgtagaaagtgacattttataatttttctgtggtcgttaatgctattttaaatgtttgtcccagGAAGGTATTTCTCTTTTTAATCGGAAGCCAACTAAAGGTATTGAGTTTCTCATCAATGCGGGTAAGGTGGGTGAATCTCCTGAAGAAATAGCAGGTTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60860.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 3
gtaagaacttaaagatgtttgtgtattatgcagattattgtagaaagtgacattttataatttttctgtggtcgttaatgctattttaaatgtttgtcccagGAAGGTATTTCTCTTTTTAATCGGAAGCCAACTAAAGGTATTGAGTTTCTCATCAATGCGGGTAAGGTGGGTGAATCTCCTGAAGAAATAGCAGGTTTTC
|| || | || || | | || | || || | | | | | | ||| | | ||| || | |||||||||| || ||||||||| ||||||| | ||||| |||||||||||||||||||| |
----------------gtaaacaaatgaacaaggttttgagaataaagtatatctttgctctagCTTTTTACCAATGAATCTAATGCTAGTGTATGGC--AGGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTCATCAATGCCAACA------------------------------------
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
gtaagaacttaaagatgtttgtgtattatgcagattattgtag-aaagtgacattttataatttttctgtggtcgttaatgctattttaaatgtttgtcccagGAAGGTATTTCTCTTTTTAATCGGAAGCCAACTAAAGGTATTGAGTTTCTCATCAATGCGGGTAAGGTGGGTGAATCTCCTGAAGAAATAGCAGGTTTTC
|| || | || || | || ||||| ||| | | | | | | | |||| | || ||| || | |||||||||| || ||||||||| ||||||| | ||||| ||||||||||| |||||||| ||||||||||| || || || |||||||| | |||||
----------------gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatgaagctaatgcaagtgtatggc--agGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 3
gtaagaacttaaagatgtttgtgtattatgcagattattgtag-aaagtgacattttataatttttctgtggtcgttaatgctattttaaatgtttgtcccagGAAGGTATTTCTCTTTTTAATCGGAAGCCAACTAAAGGTATTGAGTTTCTCATCAATGCGGGTAAGGTGGGTGAATCTCCTGAAGAAATAGCAGGTTTTC
|| || | || || | || ||||| ||| | | | | | | | |||| | || ||| || | |||||||||| || ||||||||| ||||||| | ||||| ||||||||||| |||||||| ||||||||||| || || || |||||||| | |||||
----------------gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatgaagctaatgcaagtgtatggc--agGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAACAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacattttataatttttctgtggtcgttaatgctattttaaatgtttgtcccagGAAGGTATTTCTCTTTTTAATCGGAAGCCAACTAAAGGTATTGAGTTTCTCATCAATGCGGGTAAGGTGGGTGAATCTCCTGAAGAAATAGCAGGTTTTC
cgttaat putative branch site (score: 4)
tttgtccc putative PPT
ttaatgctattttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacttaaagatgtttgtgtattatgcagattattgtagaaagtgacattttataatttttctgtggtcgttaatgctattttaaatgtttgtcccagGAAGGTATTTCTCTTTTTAATCGGAAGCCAACTAAAGGTATTGAGTTTCTCATCAATGCGGGTAAGGTGGGTGAATCTCCTGAAGAAATAGCAGGTTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA