Sequence
atgc intronic sequence ATGC exonic sequencegtatatgaatgattgtttacttaaagttttatcctttcaatgagtttgaactcaaagctaatgtgaatgaattgtgtgtttctttgcgagtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G64840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G64840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 1
gtatatgaatgattgtttacttaaagttttatcctttcaatga-----gtttgaactc----aaagctaatgtgaatgaattgtgtgtttctttgcgagtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
| ||| | | || ||| | ||||| | | | |||| |||||| | | | ||| || | | | | |||| | |||| || |||||| |||| | |||||||| |||||||| | |||||||| || |||||||||||||||| ||| | | |||| ||||| || ||||
taaaatgtctcactgagtac--actgttttgtggtgtagatgatgcgtgtttgagtgttgcaagtgttgatgataagaatgggaacttatgtttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGACACCATTGAGTGGCTTGAAGACTATCTTAACCAGCAGGATGTTCCAATGG
upper sequence: AT5G64840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0031g01640.t01 (Vitis vinifera), 3'ss of exon 1
gtatatgaatgatt--gtttacttaaagttttatcctttcaatgagt--ttgaactcaaagctaatgtgaatgaattgtgtgtttctttgcga------gtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
| |||| || |||| ||| |||||| || ||| || | ||| | | | | | || || | | | ||| || | |||| |||||||| | ||| | |||||||| |||||||| | |||||||| || ||||| ||||||||||||||| | | ||||| |||||||| ||||
---ttaaaatgtttaagttttgttagccttttatatttataatttgtactagaatgcgtggttgttattgatcggttataaatatacttgtgatcacttgcagGAGCCAGATTTATTACTATTGGATGAGCCCACAAATCACCTTGATCTTGACACAATTGAATGGCTTGAAGGTTATCTTAACAAGCAGGATGTGCCCATGG
upper sequence: AT5G64840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ10635 (Selaginella moellendorffii), 3'ss of exon 1
gtatatgaatgattgtttacttaaagttttatcctttcaatgagtttgaactcaaagctaatgtgaatgaattgtgtgtttctttgcgagtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
||| ||||||| | | ||| || | | || || | |||| || ||| | | || || || |||||||| ||||||||||| | || || ||||||||||||||||| |||||| ||||| || ||||| ||||
----------------------------gtatgctttcaagtgttcttttctcctttctgttcctcaagacaagttcaacttcc-------agGAACCTGATCTCTTACTTCTGGACGAGCCGACGAATCATTTGGACATGGACACAATTGAGTGGCTTGAAGGCTATTTGAAAAAGATCGAGGTGCCCATGG
upper sequence: AT5G64840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ35375 (Selaginella moellendorffii), 3'ss of exon 1
gtatatgaatgattgtttacttaaagttttatcctttcaatgagtttgaactcaaagctaatgtgaatgaattgtgtgtttctttgcgagtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
||| ||||||| | | ||| || | | | | ||| | | |||| || ||| | | || || || |||||||| ||||||||||| | || || ||||||||||||||||| |||||| ||||| || ||||| ||||
----------------------------gtatgctttcaagtgttcttttctcctttctgttcctcaag----gcaagttcaacttc---cagGAACCTGATCTCTTACTTCTGGACGAGCCGACGAATCATTTGGACATGGACACAATTGAGTGGCTTGAAGGCTATTTGAAAAAGATCGAGGTGCCCATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgagtttgaactcaaagctaatgtgaatgaattgtgtgtttctttgcgagtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
agctaat putative branch site (score: 3)
tgtttcttt putative PPT
aatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgaatgattgtttacttaaagttttatcctttcaatgagtttgaactcaaagctaatgtgaatgaattgtgtgtttctttgcgagtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG