Sequence
atgc intronic sequence ATGC exonic sequence...ttcaaacttttgtaaattttggttcattccatttctctttagcttctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G53660.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G53660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G40160.1 (Glycine max), 3'ss of exon 1
ttcaaacttttg--taaattttggttcattccatttctctttagcttctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG
| | || || ||||| || || || || | | || || | | | | || ||| | ||| | | | | |||||||||| ||||| ||||||||||| |||||||||||||| | || ||||| ||||||||||| || ||||||||| |||||||| | | || |||
-ctagatttatgcttaaatcgtgattggtttaatctgaggaatgaatcgaggagaaaatgtgtctgatgcatattttgtcttttcaatttgttatc-tgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
upper sequence: AT1G53660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G18730.1 (Glycine max), 3'ss of exon 2
--ttcaaacttttgtaaattttggttcattccatttctctttagcttctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG
| || || | || | | | | || | | | ||| | | ||| || | | | ||| | | | | |||||||||| ||||| ||||||||||| |||||||||||||| | || ||||| ||||||||||| || ||||||||| |||||||| | | || |||
tggttcaatttaaggaatgaataatcaaggataaaatgctgaaattctgtgttgttatgtggctgatgca-tattctgtcttttcaatttgttgtc-tgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
upper sequence: AT1G53660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g00460.t01 (Vitis vinifera), 3'ss of exon 1
-ttcaaacttttgtaaattttggttcattccatttctctttagcttctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG
|| ||| | | | | | || | | ||| | | | | ||| | | | || |||| |||| | | ||| ||||||| |||||||| ||||||||||| ||||| || ||||||||| |||| | ||||||||| || |||||||| ||||| ||| | ||||| | |
tttttttttttctttacctctctcttatccttgatatctctgtttgagctttgcttcacatggctaacagatgatttt-cttctaaaattgtaaaatgtagTGGGTTTTGTCATCAAAGGAAATAAATTTCCCCTACCCACTTGGACTGACTCTGCTTCACATGGTCTTCTCCTCTGTATTGTGCTTTATTCTCACCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG
actaatttttatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaaacttttgtaaattttggttcattccatttctctttagcttctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
-tcaaact
- - - - - - - -attttgg