Sequence
atgc intronic sequence ATGC exonic sequence...ttgagaactagcttgctggggatatcgatagtgggagcagatatcttttccacttattttaccagaatattcagtcaactaatataaatgtcatatacagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47550.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: AC209053.2_FGT002 (Zea mays), 3'ss of exon 2
ttgagaactagcttgctggggatatcgatagtgggagcag-atatcttttccacttattttacca-gaatattcagtcaactaatataaatgtcatat--acagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC-
||| | | || | | || | || | | || || ||| || ||| | | |||| | | | | ||||||||| |||| |||||||||||| ||||| ||||| |||||| ||||||| ||||| |||||| ||| | |||||||| |||| || ||| || |
----cctctaacatttcggcatttgtgcagatgaattctttatgtgcctatggtatacctttccatgacaatttaactggtgcagataactcttttttttccagTTATGTTATGGCCATTGGTGAAGCAGAGGCTTTTTCCGAAAGGATGAAGCGCGAGCTTGTAGCGCTAGAATCTGCAAATGTTTATGCC-TTGTTGGAAACT
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 6
-ttgagaactagcttgctggggatatcgatagtgggagcagatatcttttccac-ttattttaccagaatattca-gtcaactaatataaatgtcatatacagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC
|| | | || || | || | | || ||| | |||||| ||| | ||| | | || | |||| | | | || | ||||||| | ||||| ||||||||||| |||||||||||||||||| | || |||||||||| || || ||||| |||||||| ||||| ||| | |||||
ctttatca-tactttttttctaatgtgaa--gtatgagatgttatcttatcctcactatccaaaatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 6
ttgagaact-agcttgctggggatatcgatagtgggagcagatatcttttccacttattttaccagaatattcagtcaactaatataaatgtcatatacagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC
| |||| ||| | || | || | | | || | || | || || | | | | | | | | |||| ||||||||| ||||| ||||||||||||||||| |||||||||||| ||||| |||| || | || | ||||| |||||||| ||||| ||| | |||
aagccaacttagcatccttcccacattagtt-tctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcagtcatggcatgatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccacttattttaccagaatattcagtcaactaatataaatgtcatatacagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC
aactaat putative branch site (score: 2)
aactaatataaatgtc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgagaactagcttgctggggatatcgatagtgggagcagatatcttttccacttattttaccagaatattcagtcaactaatataaatgtcatatacagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC