Sequence
atgc intronic sequence ATGC exonic sequencegtttttctatagctctgagatggtgaacaaagtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24880.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os05g51550.1 (Oryza sativa), 3'ss of exon 2
------------gtt--tttctatagctctgagatggtgaacaaagtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
||| |||| ||| | | | ||| | | || ||| | || | ||| | ||| |||||||||||| || ||||| || |||||||| ||||| ||||| |||||||| | || ||| | |||||||| || || | | | | | || | |
ctgaattcaggtgttgctttcatcagcaatattgctataagtgaagacatgttgagcatttcactgagttcctaacatgttttattcatatgaacatcagGGAAGTGCTAGGCAGTTATTCCAACGACTTCAAGGACCAATAGAGGAAGAAAATCTCAAGGCACATTTTGAAAAAATGATTCTACTCATGCGGCAACTGC
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA18G36660.1 (Glycine max), 3'ss of exon 18
--------------gtttttctatagctctgagatggtgaacaaagtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
|| || | | | | | | || | | || | | || | | || | | | | | ||||| ||||| ||||||||||||||||| ||||||| ||||||||||| ||||| ||||||||||||||||| || ||| ||||||| |||| ||
attaaacctaattatttcttattttgtattatgctttcactcatacatattagtagatcctcattgtttgattggttttaaatttttgtatctttagcagGGTAGTGCCAGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 21
---------------------------------------gtttttctatagctctgagatggtga-acaaagtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
||| | || | | | | | | ||| | | || | | || | | || | | | | | ||||| ||||| |||||||||||||||| ||||||| ||||||||||| ||||| ||||||||||||||||| || ||| ||||||| |||| ||
gtaactatagagagaccaaatgattaattaaaccttattatttcttaatttttattatgcgttcacacatacatattagtagatcctcattgtttgattggttttacatttttgtatctttagcagGGTAGTGCCCGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 9
gtttttctatagctctgagatggtgaacaaagtgtcttctat-gcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
||| | || | | || | |||| || | | |||| || | ||| | ||||| ||||| || || ||||||||||| |||| |||||||||||||| ||||| |||||||||||||||||||| ||| ||||||| |||| |
--------------gtgaaaccatgtttgacatacattttgcagctttaattgggt-aaatctttcg----tatctttag----cagGGTAGTGCCAGGCAATTGTTTCAACGTTTGCAGGGGCCAATGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGC
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA16G14060.1 (Glycine max), 3'ss of exon 20
gtttttctatagctctgagatggtgaacaaagtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC-----
||||| | || ||| | ||||| ||||| || |||||||||||||| |||| |||||| ||||||| ||||| |||||||||||||||||||| ||| ||||||| |||| |
------------------------------------------------------gtaaatctttc----atatctttag----cagggtagTGCAAGGCAGTTGTTTCAACGTTTGCAGGGGCCATTGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGCATTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
aactaat putative branch site (score: 2)
tatgcttaaactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttctatagctctgagatggtgaacaaagtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA