Sequence
atgc intronic sequence ATGC exonic sequence...ttcttgataatatcataaaataagaccattacacccaaattttattttcttgtggagaagttgtttggagttacaaaatctcactagccaatcaccgcagGATCTGGACCCTCTTGAAGAAAGAAAGCGTGGGAAATGCCCTCTTACACCTCATGAAGTGGGCTTAATGCTGCGCGCTCTTGGTTTTACAAACGACACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16650.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 7
--------------ttcttgataata-tcataaaataagaccattacacccaaattttattttcttgtggagaagttgtttggagttacaaaatctcactagccaat---------caccgcagGATCTGGACCCTCTTGAAGAAAGAAAGCGTGGGAAATGCCCTCTTACACCTCATGAAGTGGGCTTAATGCTGCGCGCTCTTGGTTTTACAAACGACACAT
||| | || | ||||||| | ||| | | || || | | || | || | |||| || | | | | ||||| | | |||||| || || | || ||| | |||||||||||||| |||||||| |||||||||||||| || ||| |||| || ||||||||||||||||||||||
gtaagactgccatcctctgacttctagtaataaaattttatcatattggcaagatgataataattagttaa-aactagtttttttttgctgattttgttgagccattaccatgtggtaattcagGATTTGAGCCATGATGGAGAGCGGAAGCGTGGGAAATGTCCTCTTACTCCTCATGAAGTGGGTTTGATGTTGCGAGCACTTGGTTTTACAAACGACACAT
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G15170.1 (Glycine max), 3'ss of exon 7
-ttcttgataatatcataaaataagaccattacacccaaattttattttcttgtggagaagttgtttggagttacaaaatc-tcactagccaatcaccgcagGATCTGGACCCTCTTGAAGAAAGAAAGCGTGGGAAATGCCCTCTTACACCTCATGAAGTGGGCTTAATGCTGCGCGCTCTTGGTTTTACAAACGACACAT
|| | | | | || || | || | | || || | |||||| | ||| | | | || | | |||||| || |||| || ||| |||||||||||||| |||||||| |||||||||||||| | |||||||| || |||||||||||||| |||||||
attatggcggaagttgatccatgtagccgaccccacctagtgggataaggcgttgttgttgttgtt-gttgttgttgagccattaccttgtggtgat-acagGATTTGAGCCCTGATGGAGAGCAGAAGCGTGGGAAATGTCCTCTTACTCCTCATGAAGTGGGTCTGATGCTGCGAGCACTTGGTTTTACAAATGACACAT
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G03640.1 (Glycine max), 3'ss of exon 8
-ttcttgata-atatcataaaataagaccattacacccaaattttattttcttgtggagaagttgtttggagttacaaaatctcactagccaatcaccgcagGATCTGGACCCTCTTGAAGAAAGAAAGCGTGGGAAATGCCCTCTTACACCTCATGAAGTGGGCTTAATGCTGCGCGCTCTTGGTTTTACAAACGACACAT
| | ||| ||| | ||| || || ||||| | | || | || | | | | | | | | |||||| || ||| || |||| | ||||| |||||||| ||||||| |||||||||||||| || |||||||| || ||||| ||| |||| |||||||
ttgccatatatataagacttcttaaagttgaaactaattaactttatgctgatatgaaatgaatgagttttttcctcactcttgaatcatga--taaaacagGATTTGAGCCCAGATGGAGAACGGAAGCGAGGGAAATGTCCTCTTAGTCCTCATGAAGTGGGTTTGATGCTGCGGGCACTTGGCTTTTCAAATGACACAT
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G41740.1 (Glycine max), 3'ss of exon 7
ttcttgataatatcataaaataagaccattacacccaaattttattttcttgtggagaagttgtttggagttac--aaaatctcactagcca-atcaccgcagGATCTGGACCCTCTTGAAGAAAGAAAGCGTGGGAAATGCCCTCTTACACCTCATGAAGTGGGCTTAATGCTGCGCGCTCTTGGTTTTACAAACGACACAT
|| |||| | | | || || | | || | |||| || ||| | | || | || |||| | || | ||||||| || ||| || |||| | ||||| |||||||| |||||||| |||||||||||||| || ||||||| || ||||| ||| |||| || ||||
--ttttgccatataa-gatttcttacagttgaaactaattaactttttgctgatatgaaacgaatgagttttccctcaatcctcatgaatcatgaaaaagcagGATTTGAGCCCAGATGGAGAACGGAAGCGAGGGAAATGTCCTCTTACTCCTCATGAAGTGGGTTTGATGCTGCAGGCACTTGGCTTTTCAAAAGATACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttgtggagaagttgtttggagttacaaaatctcactagccaatcaccgcagGATCTGGACCCTCTTGAAGAAAGAAAGCGTGGGAAATGCCCTCTTACACCTCATGAAGTGGGCTTAATGCTGCGCGCTCTTGGTTTTACAAACGACACAT
atctcac putative branch site (score: 3)
ttacaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttgataatatcataaaataagaccattacacccaaattttattttcttgtggagaagttgtttggagttacaaaatctcactagccaatcaccgcagGATCTGGACCCTCTTGAAGAAAGAAAGCGTGGGAAATGCCCTCTTACACCTCATGAAGTGGGCTTAATGCTGCGCGCTCTTGGTTTTACAAACGACACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - aaaataa
- - - - - - - - - - - - - - - - acccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctagcca