Sequence
atgc intronic sequence ATGC exonic sequence...taggcgcttcggcgaagttcggttgggatactcgggtgttagttgtgaagaactgttgttaaactattatttgtgggtttaatgtgtgtgttggtgatagGTCTCTATCAAGGAGGTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 2
------taggcgcttcggcgaagttcggttgggatactcgggtgttagttgtgaagaactgttgttaaactattatttgtgggtttaatgtgtgtgttggtgatagGTCTCTATCAAGGAGGTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCC
| | | | | || | | | || | |||| | || | || | ||| || || | | || || ||||| | |||||||||||||| |||||||| ||||| || | ||||| || |||||||| ||||| ||||| | |||||||| | ||| || ||||| ||
aatatctgaatgttgcagttaaagct--tcagccttgtcctgcactagtgatttaggaggactggctg--cactatctgaaggatactttgctgaatt--caatagGCATTTATCAAGGAGGTGTATGGAAGATTAGAGTAGAATTGCCAGACGCATATCCTTACAAATCCCCATCGATCGGTTTCATCAATAAGATATATCACCC
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G150867_T03 (Zea mays), 3'ss of exon 1
------taggcgcttcggc-gaagttcggttgggatactcgggtgttagttgtgaagaactgttgttaaactattatttgtgggtttaatgtgtgtgttggtgatagGTCTCTATCAAGGAGGTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCC
| | | | ||| | | | || | | || | || ||| | | ||||| || ||| | || || || ||||| | |||||||||||| | |||| | | ||||| || || |||||||| |||||||| ||||| ||||| |||||||||| | ||| || ||||| ||
actatcttaatgttgcacttaaagcttcagtcttgtcctgcactagtgatttaggagggctg--gctgcactatc--ttatggatactttgc-tgaatt--caatagGCATTTATCAAGGAGGTATATGGAGGGTTAGAGTAGAACTGCCAGATGCGTATCCTTACAAATCCCCATCGATTGGTTTCATCAATAAGATATATCACCC
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 2
--taggcgcttcggcgaagttcggttgggatactcgggtgtt-agttgtgaagaactgttgttaaactattatttgtgggtttaatgtgtgtgttggtgatagGTCTCTATCAAGGAGGTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCC
|| | | | || | | | || || | || | |||| | | |||| |||| || | | ||||| |||||||| |||||||||||| |||| || ||||| || ||||||||||||||||| ||||||||| |||| || | | ||||||| |||||
gaattgcattaggatctatatctctagttaacttcaaaggtggaactggactaagttgtttcctttttctcattttcactttta---tgggaatcatgtgcagGTCCTTATCAAGGTGGTGTGTGGAAGGTAAGGGTGGAGCTACCTGATGCTTATCCTTATAAGTCTCCATCTATTGGCTTTGTCAACAAAATTTTCCATCC
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 2
taggcgcttcggcgaagttcggttgggatactcgggtgttagttgtgaagaactgtt---gttaaactattatttgtgggtttaatgtgtgtgttggtgat----agGTCTCTATCAAGGAGGTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCC
| | | | | || | | ||| | | | | || | | |||| || || ||| | ||| | ||| |||| | | ||||| |||||||| ||||||||||| |||| || || || || ||||| ||||||||||| ||||||||| |||| || | | ||||||| |||||
---gaattgcatttaggatctat---gtctctctgct-taacttcaaaggtgttgtttcctttgtctcatgttttatttttttcacttgtatgttaatcgtgtgcagGTCCTTATCAAGGTGGTGTGTGGAAAGTAAGGGTGGATCTACCTGATGCCTATCCTTATAAGTCTCCATCTATTGGCTTTGTCAACAAAATTTTCCATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagaactgttgttaaactattatttgtgggtttaatgtgtgtgttggtgatagGTCTCTATCAAGGAGGTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCC
gtttaat putative branch site (score: 4)
ttgttaaactattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggcgcttcggcgaagttcggttgggatactcgggtgttagttgtgaagaactgttgttaaactattatttgtgggtttaatgtgtgtgttggtgatagGTCTCTATCAAGGAGGTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCC
- - - - - - - - - - ggttggg
- - - - - - - - - - - - - - - - - - - - - - - gaagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactat