Sequence
atgc intronic sequence ATGC exonic sequencegtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcagCAACTGTGATCAGAGAGGAAGTTGGTCTTTCTCTTGACAAAGCTGGAAAAGAGGTTCTGGGTAACGCTTCCAAGGTTGTCCTGACAAAGGAAATGACAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13470.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 1
gtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcagCAACTGTGATCAGAGAGGAAGTTGGTCTTTCTCTTGACAAAGCTGGAAAAGAGGTTCTGGGTAACGCTTCCAAGGTTGTCCTGACAAAGGAAATGACAAC
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---------------------------------------gtcagttaaacttccgttctagagcatccttatgatcatgtatgctccttgtt-tataagcattctttgtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCTGACAAATCAGTCCTTGGAACAGCAGCAAAGGTTGTCCTTACTAAAGAGTCGACAAC
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G065023_T01 (Zea mays), 3'ss of exon 2
gtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcagCAACTGTGATCAGAGAGGAAGTTGGTCTTTCTCTTGACAAAGCTGGAAAAGAGGTTCTGGGTAACGCTTCCAAGGTTGTCCTGACAAAGGAAATGACAAC
||| || | || | || | || | ||| |||||| | | ||| | | |||||||||||| |||||||| |||||||| || || |||||||| || | ||| ||||| || | ||| | ||||||||||| || || | ||||||
---------------------------------------gtcagctaaacttccattctaaagcttcattttgatcatgtatgcaccttatc-cataaacatactttgtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAATCAGTTCTTGGAACAGCTGCAAAGGTTGTCCTTACGAAAGGGTCGACAAC
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 6
gtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcagCAACTGTGATCAGAGAGGAAGTTGGTCTTTCTCTTGACAAAGCTGGAAAAGAGGTTCTGGGTAACGCTTCCAAGGTTGTCCTGACAAAGGAAATGACAAC
||| || | || | || | || | ||| |||||| | | ||| | | |||||||||||| |||||||| |||||||| || || |||||||| || | ||| ||||| || | ||| | ||||||||||| || || || ||||||
---------------------------------------gtcagctaaacttccattctaaagcttcattttgatcatgtatgcaccttatc-cataaacatactttgtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAATCAGTTCTTGGAACAGCTGCAAAGGTTGTCCTTACGAAAGAGTCGACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcagCAACTGTGATCAGAGAGGAAGTTGGTCTTTCTCTTGACAAAGCTGGAAAAGAGGTTCTGGGTAACGCTTCCAAGGTTGTCCTGACAAAGGAAATGACAAC
accttac putative branch site (score: 3)
ttgcttctgttttt putative PPT
tgttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcagCAACTGTGATCAGAGAGGAAGTTGGTCTTTCTCTTGACAAAGCTGGAAAAGAGGTTCTGGGTAACGCTTCCAAGGTTGTCCTGACAAAGGAAATGACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA