Sequence
atgc intronic sequence ATGC exonic sequencegtgacaacacattacctgcttgatttgtccaatcatttcatattctaccttccatatgtctcatacaattttctgaaacagtccattgtagttgtgttgatcaatatacatttatttctaagtggttaatgaaaaactggggatatgctttcagGGGAAGGTACCGGTTTGCTCCGTCTCCATAGTACATACCGTCACGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.2 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 15
gtgacaacacattacctgcttgatttgtccaatcatttcatattctaccttccatatgtctcatacaattttctgaaacagtccattgta-gttgtgttgatcaatatacatttatttctaagtggttaatgaaaaactggggatatg--ctttcagGGGAAGGTACCGGTTTGCTCCGTCTCCATAGTACATACCGTCACGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
|||| ||||||| | || | ||| | || | | | | | ||| || | |||| | | | | | || |||| |||||||| || | || || |||||||||||||||||||| || || || |||||||||||||| ||||| ||||| |||
-------------------------------------------------------atgtttcatacaggatcatgtatt--cttattacatgtagcatcaacttgacagtggcttgtactatgtataaaggcaaaattttgtgttttaaaattgcagGAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 19
gtgacaacacattacctgcttgatttgtccaatcatttcatattctaccttccatatgtctcatacaattttctgaaacagtccattgtagttgtgttgatcaatatacatttatttctaagtggttaatgaaaaactggggatatgctttcagGGGAAGGTACCGGTTTGCTCCGTCTCCATAGTACATACCGTCACGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| || | || || ||||| | | |||| ||| ||| || ||||| ||||||| || ||| | |||| | |||||| | ||| || |||| |||||||| || | || || |||||||||||||||||||| || || || |||||||||||||| ||||| ||||| |||
---------------------gtttcatacagg-atcatgcattct---tattacatgtaacat-caactt-----gacagtgtcttgtagt-------atgtataaaggcaaatttttgtgtggttta----aaattg------------cagGAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 15
gtgacaacacattacctgcttgatttgtccaatcatttcatattctaccttccatatgtctcatacaattttctgaaacagtc-cattgtagttgtgttgatcaatatacatttatttctaagtggttaatgaaaaactggggatatgctttcagGGGAAGGTACCGGTTTGCTCCGTCTCCATAGTACATACCGTCACGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| | | || ||| ||||| | | | ||| || || || | | || | | | ||| ||| || ||| | |||| |||||||| || |||| || |||||||| ||||||||||| || ||||| || ||||||||||| ||||| ||||| |||
-------------------------------------------------tgataggtttcaaatatgatttttcattgttcttgtaatatagacatgacaatggat-tgtacc-atgcatgacatgcaaattaaattcttaa---atg-tcgcagGAGAAGGTACAGGGCTGCTTCGCCTCCATAGCACATACCGTCATGATCTTAAGATATACAGCTCTGATGAGGGTCGTGTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaatatacatttatttctaagtggttaatgaaaaactggggatatgctttcagGGGAAGGTACCGGTTTGCTCCGTCTCCATAGTACATACCGTCACGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
ggttaat putative branch site (score: 4)
tgctttc putative PPT
tatacatttatttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacaacacattacctgcttgatttgtccaatcatttcatattctaccttccatatgtctcatacaattttctgaaacagtccattgtagttgtgttgatcaatatacatttatttctaagtggttaatgaaaaactggggatatgctttcagGGGAAGGTACCGGTTTGCTCCGTCTCCATAGTACATACCGTCACGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC