Sequence
atgc intronic sequence ATGC exonic sequencegtaaatggtaaaaaagctgtaatattttcatttcacaaaaaaatgggtttgatgacacttaggtttatgttttttcattggtgagaagTGAGTGATGAAGGAGAAAACTGGAGCGTGGGACAGAGACAACTGTTCTGTCTTGGAAGAGTACTGTTAAAGAGAAACAAAATATTAGTGTTAGATGAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21250.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G20770.2 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------------------------------------gtaaatggtaa-aaaagctgtaatatt------ttcatttcacaaaaaaatgggtttgatgacacttag--gtttatgttt---tttcattggtgaga-agTGAGTGATGAAGGAGAAAACTGGAGCGTGGGACAGAGACAACTGTTCTGTCTTGGAAGAGTACTGTTAAAGAGAAACAAAATATTAGTGTTAGATGAAGC
|| || | | | | |||| | || |||| ||| |||| || || || | | |||| || | || | | | | || | | |||||||||||| |||| ||| |||||| |||||||| | |||||||| ||||||||||||||||| | ||||| |||| ||| | || ||||||||||
gtgagtaaacttctagccaattctctctgcagccttgggcaagaatctattgctgctttactcttttgaggtttaactttaggaggaattcaaaatcatagttgttcttacatgttgtacttttaaagcattcaattcgcaaattaagaaattggaaca-atttagctattgaagtctaattctgacaagttatacagTGAGTGATGAGGGAGGAAATTGGAGCTTGGGACAGCGCCAACTGTTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATTCTTGTTCTAGATGAAGC
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G01390.1 (Glycine max), 3'ss of exon 11
-----gtaaatggtaa--aaaagctgtaatattttcatttcacaaaaaaatgggtttgatgacacttag--gtttatgttt---tttcattggtgaga-agTGAGTGATGAAGGAGAAAACTGGAGCGTGGGACAGAGACAACTGTTCTGTCTTGGAAGAGTACTGTTAAAGAGAAACAAAATATTAGTGTTAGATGAAGC
| || | | | | ||| ||| || |||| | |||| | |||| || | || | | | | | | | | ||||||||||||||| | ||| |||||| |||||||| | ||||| || ||||||||||||||||| | ||||| |||| ||| |||| | ||||||||
atgttgaaacttacattttgtacttttaaagcactcaatttccaaattag-aattttggaacaaattagttattgaagtctaattctgactaattacacagTGAGTGATGAAGGTGGAAATTGGAGCTTGGGACAGCGCCAACTATTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATTCTAGTTCTGGATGAAGC
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G20780.1 (Glycine max), 3'ss of exon 11
--------gtaaatggtaaaaaagctgta-atatttt-catttcacaaaaaaatgggtttgatgacacttaggtttatgtt-ttttcattgg-tgagaagTGAGTGATGAAGGAGAAAACTGGAGCGTGGGACAGAGACAACTGTTCTGTCTTGGAAGAGTACTGTTAAAGAGAAACAAAATATTAGTGTTAGATGAAGC
| | | | ||| | || | || | | ||| ||| || ||| | | | | | || | | | | ||||||||||||||| ||||||||||| ||||||||| | ||||| | ||||| |||||||| || | ||||| |||| ||| | || | ||||||||
gactgcatattagtcaaattaaaattttacacatataatgtatcaacaaacaaaaattttactcctgactgaaatagtctaattctgaccaacttaacagTGAGTGATGAAGGTGAAAACTGGAGTGTGGGACAGCGTCAACTCATATGTCTCGGAAGAGTGCTTCTTAAGAGGAACAGAATTCTTGTTCTGGATGAAGC
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G20360.1 (Glycine max), 3'ss of exon 10
--------------------------------------------------------------------------gtaaatggtaaaaaagctgtaatatttt-catttc-acaaaaaaat---gggtttgatgacacttaggtttatgttttttcattggtgagaagTGAGTGATGAAGGAGAAAACTGGAGCGTGGGACAGAGACAACTGTTCTGTCTTGGAAGAGTACTGTTAAAGAGAAACAAAATATTAGTGTTAGATGAAGC
||||| ||| | || || | ||||| || ||| || | || | | | | | | || | ||| | ||||||||||||||| | ||| |||||| ||||||| |||||||| ||||||||||||||||| | ||||| |||| |||| | || |||| |||||
gtgagttaacaaacctgaagccaacaatctgatgtacttttatataagtcactattctactctttcaacattaagtaaaatacaaagtaatcatatagttctgcatttttacccaaagatcttgcaacaaataaaccattgaagtctaattctgagttgttattcagTGAGTGATGAAGGTGGAAATTGGAGCTTGGGACAACAGCAACTGTTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATACTTGTTCTAGACGAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacaaaaaaatgggtttgatgacacttaggtttatgttttttcattggtgagaagTGAGTGATGAAGGAGAAAACTGGAGCGTGGGACAGAGACAACTGTTCTGTCTTGGAAGAGTACTGTTAAAGAGAAACAAAATATTAGTGTTAGATGAAGC
gtttgat putative branch site (score: 5)
ttttttcatt putative PPT
tttatgttttttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatggtaaaaaagctgtaatattttcatttcacaaaaaaatgggtttgatgacacttaggtttatgttttttcattggtgagaagTGAGTGATGAAGGAGAAAACTGGAGCGTGGGACAGAGACAACTGTTCTGTCTTGGAAGAGTACTGTTAAAGAGAAACAAAATATTAGTGTTAGATGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC