Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagttgggactggcatcttatggaattggtatgcataatctcactttactggtcatttactttgggacagAAAGGAACAGTTGTCGAGAAACTCACGGAGGAAACTCTGCGGGACTGGAATCATTTTAAGGAGCTTTTATCAATCTGTATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51150.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g35890.1 (Oryza sativa), 3'ss of exon 5
----------------gtaaaagttgggactggcatcttatggaattggtatgca--taatctcactttactggtcatt-tactttgggacagAAAGGAACAGTTGTCGAGAAACTCACGGAGGAAACTCTGCGGGACTGGAATCATTTTAAGGAGCTTTTATCAATCTGTATAG
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gttacctttttccttgacatggtttgctgattaccttcaacaaaaatcctgcaaaatttatcacattttgctgttctttctgaatgcaaacagAAAGGAACAGTTGTAGAAAAACTCACCGAGGAGACTCTGCGAGACAAAGGCCATCTTCTGGAGCTCCTTGCTGTGTGTGAAG
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 4
----------------------gtaaaagttgggactggcatcttatggaattggtatgcataatctcactt---tactggtcatt-tactttgggacagAAAGGAACAGTTGTCGAGAAACTCACGGAGGAAACTCTGCGGGACTGGAATCATTTTAAGGAGCTTTTATCAATCTGTATAG
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gtgaactgctcttgaaggttacctaaaaaaggatgcaaatttcttacgtgtatgtcaagctcatgtttatctacatgtgtgccattcttgatctggtcagAAAGGAACTGTGGTAGAGAAACTCACCGAGGAAACTCTCAAGGACAAAGGCCATCTCTTGGAGCTCCTTGCAGTGTGTGAAG
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaagttgggactggcatcttatggaattggtatgcataatctcactt----tactggtcatttact-ttgggacagAAAGGAACAGTTGTCGAGAAACTCACGGAGGAAACTCTGCGGGACTGGAATCATTTTAAGGAGCTTTTATCAATCTGTATAG
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------gttag--ttcccttctcaatgtaccaactagtatatttatatttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttatggaattggtatgcataatctcactttactggtcatttactttgggacagAAAGGAACAGTTGTCGAGAAACTCACGGAGGAAACTCTGCGGGACTGGAATCATTTTAAGGAGCTTTTATCAATCTGTATAG
atctcac putative branch site (score: 3)
tttacttt putative PPT
atttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagttgggactggcatcttatggaattggtatgcataatctcactttactggtcatttactttgggacagAAAGGAACAGTTGTCGAGAAACTCACGGAGGAAACTCTGCGGGACTGGAATCATTTTAAGGAGCTTTTATCAATCTGTATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT