Sequence
atgc intronic sequence ATGC exonic sequence...tttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 1
-tttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgtttt---gattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
||| ||| | | | ||||| | | | || || ||| || | | | |||||| || | || | ||| ||| | ||||| ||||| | || || |||||||| |||||||| || |||||| ||||||||||||||| || |||||||| || ||| |||| |||||||| | | || | |
atttcaggttcctgttataaattttgtctatatttttttaatagaattttttttatataatagattaaataatgga--tggtacttat-tcattgtta-agcagATCTCGTCGTTCAGAGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACGGCCACAAAGACTCTCCATCTGAGAACTGATTCGAGGAAGGACCGTG
upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 1
-----tttgtggtcacaactttcttt----tttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
| | | | | | | || ||| |||| || |||||| ||| || |||| | || ||| | | || | || ||||| | || || ||||| || |||||||| || |||||| |||||||||||||||| |||||||||| || ||| |||| || ||||| | | || | |
gataatataaaattatatatgccattaaatttttttttttcagtagaaaataaaa---------ttggatttaatagatgaataatgatacttattcattgttaagcagATCTCGTCATTCAGGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTG
upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G04340.1 (Glycine max), 3'ss of exon 2
tttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG--------------
| | || |||| |||| || |||||| ||| || |||| | || ||| | | || | || ||||| | || || ||||| || |||||||| || |||||| |||||||||||||||| |||||||||| || ||| |||| || ||||| | | || | |
-----atatatgccattaaatttttttttttcagtagaaaataaaa---------ttggatttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA
upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 1
tttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttga----ttaagtac-ttgagcttgtaactatgtt---tttgt-ttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
|||| || | ||||| |||| ||| | | | ||| | || | |||| ||| | || || | | || ||||| |||| || || ||||| |||||||| |||||| | ||||||||||| |||||||| |||||||| ||| |||| |||||||| | | ||| | |
--------tgttccttttaattattctttttcaacgaaaaac-aaacttggttagagtgagtttcttcgtgcattgaaattgaagttacattgcgtgaatgtttagcagATTTCGTCGTTTAGAGAGAGCAAGTCAGATGATCGGCGTTTCTATATATTTACAGCAACGAAGACCCTCCATCTGAGAACTGATTCAAGGAAAGATCGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
ttgtaac putative branch site (score: 2)
tttttgtttc putative PPT
ttttgattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
- - - -tcacaac
- - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - gaaaact