Sequence
atgc intronic sequence ATGC exonic sequence...gaaattttggatattgaaatgatttttttagttggttttgagtgttctgcttttgtagattaggacagttgtgaatgacttgtaactatgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66880.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 1
gaaattttg---gatattgaaatgatttttttagttggttttgagtgttctgctt-ttgtagattaggacagttgtgaatgacttgtaactatgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
| |||||| | |||| || | || | | | ||| ||||| ||| || ||||| ||| ||| | || | | |||||||||||||||||| | ||||| |||||||| |||||||| || ||||||||||| ||||| ||||||||||||
gcaattttttacggcattggtttgctgttagtttcttactctgatgaagttgcttactgtttttttttttttttgtgtatgg--tgttgttgtgtg--tcgcagATTGATGAAAATGTAAAGAGGGAAATCATTAATCACAGGTCTCTGAGGCATCCTAACATTGTTAGATTTAAAGAG
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G20610.3 (Glycine max), 3'ss of exon 1
gaaattttg---gatattgaaatgatttttttagttggttttgagtgttctgctt-ttgtagattaggacagttgtgaatgacttgtaactatgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG-------------------------
| |||||| | |||| || | || | | | ||| ||||| ||| || ||||| ||| ||| | || | | |||||||||||||||||| | ||||| |||||||| |||||||| || ||||||||||| ||||| ||||||||||||
gcaattttttacggcattggtttgctgttagtttcttactctgatgaagttgcttactgtttttttttttttttgtgtatgg--tgttgttgtgtg--tcgcagATTGATGAAAATGTAAAGAGGGAAATCATTAATCACAGGTCTCTGAGGCATCCTAACATTGTTAGATTTAAAGAGGTTGGTTATGTTTTTCAAATATTTA
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 1
gaaattttggatattgaaatgatttttttagttggttttgagtgttctgcttttgtagattaggacagttgtgaatgacttgtaact--atgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
|| | || | || |||| || |||| | | || || | | || | | || | | | | | | | || | || |||||||||||||||||| |||| || |||||||| |||||||| ||||| |||||||| ||| |||| ||||| |||
--aagtatgatcaaagatcaacttttatttgttgccagtttctttttcttgttgatgaagcagtagacttatctcttccctatcattcgttgtgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 1
gaaattttggatattgaaatgatttttttagttggttttgagtgttctgcttttgtagattaggacagttgtgaatgacttgtaact--atgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
|| || | || | | ||| || || | | || || | | || | || | | | | | | | || | || |||||||||||||||||| |||| || |||||||| |||||||| ||||| |||||||| ||| |||| ||||| |||
--gatcttttagatcaatctttatttgttgccactttctttctttttcatgttgatgaagcagtggacttatctcttccctatcatttgctgtgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 1
gaaattttggatattgaaatgattttttta----gttggttttgagtgttctgcttttgtagattag--gacagttgtgaatgacttgtaactatgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
| | | ||| | ||| ||| || |||| | || | | || | | | | | ||| | | | | ||| | | | |||||||||||||||||| | ||||| || || || |||||||| || ||||||||||| ||||| || |||||||||
------ctttttttagaatttttttccttacggcattcgtttggtgtttcttactctgatgaagttgctgactgattttttttgtgtgtgttgttttgtctcgcagATTGATGAAAATGTGAAGAGGGAAATTATCAATCACAGGTCTCTGAGGCATCCTAACATTGTTAGGTTTAAAGAG
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 1
----gaaattttggatattgaaatgatttttttagttggttttgagtgttctgcttttgtagattaggacagttgtgaatgacttgtaactatgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
| | ||| |||| | ||||| | | | | || | | || || | ||| ||| | | | | || ||| | |||||||||||||||||||||||||||||| || ||||| || ||||| || ||||| || || ||||| || |||||||||
tgaagccaatttagatag-gctatgatatccaccttggttatttaattttatgaatatgtt--ttaaaatgtggatttctca-ttataatattctttgttgcagATTGATGAAAATGTTCAAAGGGAAATAATTAATCATAGGTCTCTCAGGCACCCCAACATTGTTAGGTTTAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgcttttgtagattaggacagttgtgaatgacttgtaactatgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
ttgtaac putative branch site (score: 2)
ttttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaattttggatattgaaatgatttttttagttggttttgagtgttctgcttttgtagattaggacagttgtgaatgacttgtaactatgggagttgcagATTGATGAAAATGTTCAAAGGGAGATCATTAACCACAGGTCACTAAGGCATCCTAATATTGTCAGATTTAAAGAG
- -attttgg
- - - - - - - - - - - - - - - - -ggttttg