Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgtgatataagggtccgaaagttgcagacagatacgattttaagtctttttatctgacacaagtatacgttggactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28850.1 |
intron # | 8 |
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 8
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
--------------------gtaagttgtgatataagggtccgaaagttgcagacagatacgattttaagtctttttatctgacacaagtatacgttg-gactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
||| | | | | | ||| ||| | | | || | | ||| || | | | || || |||||| |||||||| || ||||||| |||||| || | || || ||||| ||||||| |||||||| ||||| |||||| |||||||||||||||| |||
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttg---atctttgtggttgactat-tagctatttgtgatttg-acgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
-----------------gtaagttgtgatataagggtccgaaagttgcagacagatacgattttaagtctttttatctgacacaagt---atacgttg-gactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
||| | | | | | ||| ||| || | | || | |||| ||| || | || || || |||||| |||||||| || ||||||| |||||| || | || || ||||| ||||||| |||||||| ||||| |||||| |||||||||||||||| |||
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttg---acctttgtggtt--gactcttgttagctatttgtgatttgatgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
----------gtaagttgtg-atataagggtccgaaagttgcagacagatacgattttaagtcttt------ttatctgacacaagtatacgttggactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
|||| ||| |||| | || | | | ||||||||| | | ||||| | || | |||||| ||||||||||| ||||||| |||||| || |||| | ||||| ||||||| |||||||| ||||| |||||| | ||||| |||||||| |||
atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcact-attagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagacagatacgattttaagtctttttatctgacacaagtatacgttggactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
atctgac putative branch site (score: 3)
attttaagtcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgtgatataagggtccgaaagttgcagacagatacgattttaagtctttttatctgacacaagtatacgttggactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG