Sequence
atgc intronic sequence ATGC exonic sequencegtgtgaccatttctcagtttctctatgttgttaaaccattactgtaatatttcaagtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55060.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G43140.1 (Glycine max), 3'ss of exon 9
gtgtgaccatttctcagtttctctatgttgttaaaccattactgtaatatttcaa-gtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
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tttggaagaaacatgggcattgttatggcgacttgccac-attatgtctttttgatatcatat----aagggaactttgctgaattctccattacatattggtagGTAATTTGTGGCGTGAATTGTGGGAAACATCTAAACCAGTTCCAGCTGTTAAACAGGCACCTCTCTATGATGAGGATTTGGCAGT
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G46190.1 (Glycine max), 3'ss of exon 10
gtgtgaccatttctcagtttctctatgttgttaaaccattactgtaatatttcaagtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
| | | || | | | || | | | || | || || | |||| || ||| | | | | || | | | |||||||||| |||||||| ||||||||||| | |||||| | ||||||||||| || |||||||| |||||||| ||||| || |
-ttttattataagttataacacaaaatctgcaaga--aatatgggaactgttgagcatttattttcttctgatttcat-attattaaacttgtctgaattgtagGTAATTTGTGGCGTGAATTGTGGGAAACATCCAAACCAGTACCTGCTGTTAAGCAGGCACCTCTGTTTGATGAGGATTTGGCATT
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G02550.1 (Glycine max), 3'ss of exon 10
gtgtgaccatttctcagtttctctatgttgttaaaccattactgtaatatttcaagtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
|| | || | | | | | || | || | || || | |||| || ||| | | | | || || | | | ||||||||||||||||||| ||||||||||| | |||||| | ||||||||||| || || ||||| |||||||| ||||| || ||
--gttataataagttataacacacaaaatctgcaagaaatatgggaactgttgagcatttattttcttctgatttcat--attattaaactatccgaattgtagGTAATTTATGGCGTGAATTGTGGGAAACATCCAAACCAGTACCTGCTGTTAAGCAGGCGCCTCTGTTTGATGAGGATTTGGCAGT
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G10700.1 (Glycine max), 3'ss of exon 4
gtgtgaccatttctcagtttctctatgttgttaaaccattactgtaatatttc---aagtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
|| || || | || | |||| | | ||| | | | | | | ||| | || | | ||||| |||||||||| |||||||| ||||||||||| ||||| || | || ||||||||||| ||||||||| |||||| |||||||| ||
-------tataaaacatgttttgtaagaaacatgggcattgttatggccattcgccactttatgtgtttttgggaactttgctgaattctcctttacatattggtagGTAATTTGTGGCGTGAATTGTGGGAAACATCTAAATCAGTTCCAGCTGTTAAACAGACACCTCTCTATGATGAGGATTTAGCAGT
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 10
gtgtgaccatttctcagtttctctatgttgttaaaccattactgtaat-atttcaagtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
| || || | |||||| || || || ||| | | || | | || ||| || | | | || | | | || | ||||||||| ||| |||| |||||| | ||||| |||||| | || ||||||||||||||||| ||||||||||| ||||| || ||
atatg-ttatgcttagaggcctctata--agtagac--ttgctgaacttatctggaatcacattaacagattgctctgataaaatgactactcattgatattcagGTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaagtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
gtcttac putative branch site (score: 3)
ttaccaacgttttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgaccatttctcagtttctctatgttgttaaaccattactgtaatatttcaagtcgtattctcaactggtcttaccaacgttttaaaaaaaatattattagGTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA