Sequence
atgc intronic sequence ATGC exonic sequencegttgggttatcagttcatgagttctcctatatgagtaggtgtgctggtttattttaccgattgactgtatttgttcttttctgtagTTGTTGGAACTGTTGAAGGTGGAAGAGCTCCAACCAAAATTAAGACAGATTTGAAGAAACCAATTGTGAACATTGCTTGCCATCCTCGACTACCTGTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50590.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G10590.1 (Glycine max), 3'ss of exon 3
------gttgggttatca-----gttcatgagt---tctcctata---tgagtaggtgtgctggtttattttaccgattgactgtatttgttcttttctgtagTTGTTGGAACTGTTGAAGGTGGAAGAGCTCCAACCAAAATTAAGACAGATTTGAAGAAACCAATTGTGAACATTGCTTGCCATCCTCGACTACCTGTCCT
||| |||||| || || | | | | | || ||| || || || | || | | | |||| |||| | | || ||||||||||||||||||||| || ||||| || || ||||| |||||||| |||||||| || ||||| ||| ||||||| |||||||| || ||||| ||
gttggctctggtttatcatatgtgtagataaatgtgtttgttgtagtttgattactaatggtgatgatttgtgttaaatatctgtttttg--cataaatgaagTTGTTGGAACTGTTGAAGGCGGTAGAGCACCCACGAAAATCAAGACAGACTTGAAGAAGCCTATTGTTAACCTTGCTTGTCATCCTCGCCTCCCTGTACT
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G39110.1 (Glycine max), 3'ss of exon 3
---------------gttgggttatcagttcatgagttctcctat-atgagtaggtgtgctggttt----attttaccgattgactgtatttgttcttttctgtagTTGTTGGAACTGTTGAAGGTGGAAGAGCTCCAACCAAAATTAAGACAGATTTGAAGAAACCAATTGTGAACATTGCTTGCCATCCTCGACTACCTGTCCT
| | | | | || || || | | ||| | | || | | ||||| | | | | ||| | | || ||||||||||||||||||||| || ||||| || || ||||| |||||||| |||||||| || |||||||| ||||||| |||||||| || ||||| ||
gttggatgtctgatttcttatctgtgaagttatacgtgctattgtcgccagttcgattactaatcttgagattttttgggctatatctgtttttgcacaaatgaagTTGTTGGAACTGTTGAAGGCGGTAGAGCACCCACAAAAATCAAGACAGACTTGAAGAAGCCTATTGTGAATCTTGCTTGTCATCCTCGCCTCCCTGTTCT
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G20310.1 (Glycine max), 3'ss of exon 3
---------gttgggttatcagttcatgagt---tctcctata---tgagtaggtgtgctggtttattttaccgattgactgtatttgttcttttctgtagTTGTTGGAACTGTTGAAGGTGGAAGAGCTCCAACCAAAATTAAGACAGATTTGAAGAAACCAATTGTGAACATTGCTTGCCATCCTCGACTACCTGTCCT
||| | || || || | | | | | || ||| || || || | |||| | | |||| | || | | || ||||||||||||||||||||| || ||| | || || ||||| |||||||| |||||||| || ||||| ||| ||||||| |||||||| || ||||| ||
gttggctctgttttatcatgtgtagataaatgtgtttgttgtagtttgattactaatggtgatgatttttgttaaatatctgtttctg--cataaatgaagTTGTTGGAACTGTTGAAGGCGGTAGAACACCCACGAAAATCAAGACAGACTTGAAGAAGCCTATTGTTAACCTTGCTTGTCATCCTCGCCTCCCTGTACT
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0379g00020.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------gttg-ggttatcagttcatgag--ttctcctatat-gagtaggtgtgctggtt-tattttaccgattgactgtattt---gttctt-------ttc------tgtagTTGTTGGAACTGTTGAAGGTGGAAGAGCTCCAACCAAAATTAAGACAGATTTGAAGAAACCAATTGTGAACATTGCTTGCCATCCTCGACTACCTGTCCT
||| |||| | | | ||| |||| | ||| |||| |||| | || | |||| | | || || ||||| ||| || ||||||||||||||||||||| || ||||| ||||| ||||| ||||||||| |||||||||| |||| || |||||||||| || || || ||||||||
gtttgatgttacttcctatagttatcattcactgaatagttttgcagttatggttgttaaattttgaagtttctgttgtatcaagtacctgtgttctttatgtttttgtgcctagtagtgcttctaattcttgaattgtttcactgcatgaagTTGTTGGAACTGTTGAAGGGGGGAGAGCACCAACAAAAATAAAGACAGATCTGAAGAAACCTGTTGTCAATCTTGCTTGCCACCCCCGCCTTCCTGTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagtaggtgtgctggtttattttaccgattgactgtatttgttcttttctgtagTTGTTGGAACTGTTGAAGGTGGAAGAGCTCCAACCAAAATTAAGACAGATTTGAAGAAACCAATTGTGAACATTGCTTGCCATCCTCGACTACCTGTCCT
gattgac putative branch site (score: 3)
tatttgttcttttct putative PPT
tttatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggttatcagttcatgagttctcctatatgagtaggtgtgctggtttattttaccgattgactgtatttgttcttttctgtagTTGTTGGAACTGTTGAAGGTGGAAGAGCTCCAACCAAAATTAAGACAGATTTGAAGAAACCAATTGTGAACATTGCTTGCCATCCTCGACTACCTGTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA