Sequence
atgc intronic sequence ATGC exonic sequence...taaatctgattgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaatgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G70450.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G03690.1 (Glycine max), 3'ss of exon 6
---taaatctgattgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaatgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
| || | || || | | | | || | | | || || | || || | || | | |||| || ||||||| |||| |||||||||||| ||||||| || | || |||||||||||||||||||| ||||||||||| ||| | ||||||||||||||| | |||
ttttgaagtttataatggaaactttat---cagggaaaaccttcagtaatgccaaatgctaaactaaactaccacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
upper sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G39480.1 (Glycine max), 3'ss of exon 7
taaatctg-attgtgatgaactagtacgtatagagaggttaagaggttataa-attgttgaaaagtacataagcctctaatgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
||| || | | || | ||| | || || || | || | ||| || | | | | | | | | | ||| | |||||||| |||| |||||||||||| ||||||| || | || |||||||||||||||||||| ||||| ||||| ||| | |||||| |||||||| | |||
-aaacatgtagttcaataatgtag-atacatttgctggaaaaccttcttcaataatgtccaataaaattactacaccaactcgtttctgactttaatttcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACGGATAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACTGGAAGGAAA
upper sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G04010.1 (Glycine max), 3'ss of exon 6
taaatctga--ttgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaa-tgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
| ||| || | ||| | | | ||| | | | || || | || | || |||| | | |||| || ||||||| |||| ||||| |||||| ||||||| || | || |||||||||||||||||||| ||||||||||| || | ||||||||||||||| | |||
---gtttgagtttataatggaaacattatcaaagaaaaccttcagtaatgccaaatgctaaactaaaactatcatactaactcattctagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
upper sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G19100.1 (Glycine max), 3'ss of exon 5
taaatctgattgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaa---tgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
|||| | | | ||| | | | | | || || || | ||| | || || || | || || ||||| ||| ||||||| |||| |||||||||||| ||||||| || | || || ||||||||||||||||| ||||| ||||| ||| | |||||| |||| ||| | |||
-aaatattttaataatgtagatgcatttgccggccgga-aaacctttttcaataatgcccaattaaattactacagaaactcatttctggcttcaatta-cagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
upper sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0127g00670.t01 (Vitis vinifera), 3'ss of exon 5
taaatctgattgtgatgaactagtacgtatagagaggttaagaggttat---aaattgttgaaaagtacataagcctctaatgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
| | || || | || | | | ||| | | ||| | |||| | || | ||||||| || ||| | | |||||||| |||||||||| |||||| |||||| || | ||||||||||| ||||| ||||| || || || || || |||||||||||||| || || |||
aataagggaaagtaagaaagagctgcaattcaagatttccaactgttctcctaaatgcatctctggtgattgtcatactaatgtc-cag--tttggctttcagGTACATGGCACCAGAGTATGCATCAAGTGGGAAATTGACTGATAGATCTGATGTATTCTCATTCGGGGTGGTACTTTTAGAGCTTATAACAGGGCGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataaattgttgaaaagtacataagcctctaatgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
ctctaat putative branch site (score: 3)
cttttgtt putative PPT
taatgttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaatctgattgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaatgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acataag