Sequence
atgc intronic sequence ATGC exonic sequencegtggttcatacatttcgttctttacactccttatgatgtaactttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19010.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 6
------------gtggttcatacatttcgttctttacactccttatgatgtaactttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA
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gtattgtcagtattagcatcaaccttgcatctttttttttttttggtgtgttatctcaagtgtcagcagctaat--gtagcagccacattttcagGCGCTTGCTGATCCTTATTTCAAGAACATAGCCAATGTTGATAGAGAGCCTTCTGCTCAACCTATCACAAAGCTAGAGTTTGAGTTCGAGAGGCGGAGAA
upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 6
gtggttcatacatttcgttct-ttacactccttatgatgtaactttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA
|| ||| ||| | || | || | | | || ||| | | | | | | || | | || || | | |||||| ||||| ||| || |||| |||| || || || ||||| ||||| || || ||||| |||||| |||||||||||||||||||| ||||||
gtacaacat-catccctttttattttatttttaatcatggtaatctaaa-acaacaaaagataatgtattgtacatattttcagGCTCTTGCCGATCCTTATTTCAGAAACATAGCAAATGTAGATAGAGAACCTTCAGCACAGCCTGTGACAAAGCTGGAATTTGAGTTTGAAAGGAGGAGGA
upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 5
gtggttcatacatttcgttctttacactccttatgatgtaactttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA
||| || ||| || |||| | | | | | ||||| | || || ||| | |||| ||||| ||||| || || || ||| | |||| || || || |||||||||||||| ||| ||||||||||| | ||||||||||| || || |||||
gtgattt-tactgacagtcttttag--tacatgttct-caacttc--tcatgcacaagctgatg-tcttatacacattgccagGCTCTTGCTCATCCTTATTTTAAGAATATAGCCAATGTGGATAGAGAGCCTTCTGCACAAGCTGTCACAAAGCTCGAATTTGAGTTCGAGAGACGGAGAG
upper sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------gtggttcatacatttcgttctttacactccttatgatgtaac--tttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA
||| | ||| | | | | | || ||||| | || | || | | | || | | |||| |||||| ||||||||| || || || |||||||| |||||||| ||||| || ||||||||||| || || |||||||||||||| ||||| ||| | ||||
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgtt--ttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttatgatgtaactttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA
aactaaa putative branch site (score: 2)
ttacctc putative PPT
taactaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggttcatacatttcgttctttacactccttatgatgtaactttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA