Sequence
atgc intronic sequence ATGC exonic sequence...catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagttcctttgtatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22350.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 2
catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagttcctttgtatgaaggcttcgg--tgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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------------------gtgcttttctatcgt----cgcccatgttaactctagtaatgagctcagagctatgcagttttttgattggtgtgctttggcagGTTTACAACAGAGCAGGTTCGTAATCTTGATAGGAACAAGCAGTGGTCTAGAGCTCTTGATGGCTCCAATTATCTACCTGGAATG
upper sequence: AT4G22350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagttcctttgtatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
|||| ||| ||||| ||| | ||||| ||| || | | | || | || || | | | |||||| | || | || || | |||||||| |||| |||||||||||| || |||||||||||| | ||||| || ||||||
-----gtgcttcttcat----tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttc--tggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
upper sequence: AT4G22350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 3
-catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagttcctttgtatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
| | || || | || | || | | ||| || | | | | | | | | | | | | |||| || | ||| || | | | | |||| | | |||||||| |||| |||||||||||||||||||||||| || || ||||| ||||||
attctctgttctctttatgttgttgttaccttgaattctttaaatgattaactactaatatgcattatctaagttcattcatatg-gttatctatctgcagATTCACTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCCGGAATG
upper sequence: AT4G22350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 3
catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagt-tcctttgtatgaaggcttcggtg---ctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
|| || | ||| || | | | || | || || | | | | | | | | | | | | || | || || | ||| || | | | |||| | | |||||||| |||| |||||||||||||||||||||||| || || ||||| ||||||
----attctctgttctctttatgctgttgttaccttgaattctttaactgttaaactactaatatacatgatctaagttcattcatgtggttctctatctgcagATTCGCTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCTGGAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctttgatttttcagttcctttgtatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
ctttgat putative branch site (score: 5)
tccattt putative PPT
ttgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagttcctttgtatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
- - - - - -gaacata
- - - - - - - - - - -ctcttct
- - - - - - - - - - - - - - - - tgttttg