Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29160.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G05700.2 (Glycine max), 3'ss of exon 3
gtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatcc---gaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG-----------------------------
|| || | | | ||||| | | ||| | |||| | ||| | ||| | ||| || | || ||||||| |||||||| |||||||| || | |||||||| || ||||||||||||||||||||||||||||| ||||| || | | ||| || |||||||
-------------gtataatttgtaatatttttgt-gtgcttcag---agatttgtgcttgccacattattgaatccaacttatgttatgaaaacagataatttctggtgtggagtactgtcacagGAATATGGTGGTTCATAGAGACCTGAAGCCTGAGAATTTACTCTTGGACTCAAAATTTAACATCAAGATTGCTGATTTTGGGTTGAGCAACATCATGCGT
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 3
gtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcat---atccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG
|| || | | | ||||| | | ||| | |||| | ||| | ||| | ||| || || || ||||||| |||||||| |||||||| || | |||||||| || ||||||||||||||||||||||||||||| ||||| || | | ||| || |||||||
-------------gtataatttgtaatatttttgt-gtgcttcag---agatttgtgcttgccacattattgaatccaacttatgttatgaaaacagATAATTTCTGGTGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGACCTGAAGCCTGAGAATTTACTCTTGGACTCAAAATTTAACATCAAGATTG
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 3
----gtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG
| |||||| || ||| ||| | || | |||||||| || ||| | | || | ||| | | | ||||||| |||||||| |||||||| || | |||||||| || |||||||| ||||||||||||||||||| ||||| || | |||||| | |||||||
gtaggattgtttactattttgtgtaattaagagactttt------tcatgtcaca---gattttccaagctaatt---tctgattt---tggaagcagATAATCTCTGGTGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
----gtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG
| |||||| || ||| || | |||| | | ||| || ||| | | | | || || || | ||||||| ||||| || |||||||| || | |||||||| || |||||||| ||||||||||||||||||| ||||| || | |||||| | |||||||
gtaggattgtttactattttgtgtagtgaagacttttg---cttgtcacag-atttttcaagctaatttctgattttgg-------------aagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG
gtttgac putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC