Sequence
atgc intronic sequence ATGC exonic sequencegtaatcctttctctttgattacacttgatcttgaaattaatgtctcctaaaggttaagcttgtaaatatgtagGTGGGGTTGAACAACATACAAAAGACAGAGTTTGTGAATGTTACAATCCAGTCGTTGATGAGAGTTACTCCTCTAAGGAATTTCTTCCTCATTCCTGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22350.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 3
--------------------------------gtaatcctttct-ctttgattacacttgatct-tgaaattaatgtctcctaaaggttaagcttgtaaatatgtagGTGGGGTTGAACAACATACAAAAGACAGAGTTTGTGAATGTTACAATCCAGTCGTTGATGAGAGTTACTCCTCTAAGGAATTTCTTCCTCATTCCTGAAA
| ||| || ||| |||||| | || || || | || | || || || |||| |||| || |||| || | |||||||| | ||||||| ||||||||||| ||||| ||||| || |||||| |||||||| |||| |||||||| ||||| |||||||
cattgcagatttcctattgcacctcaatatttgcaattctctctgctttgaccattattatcctatggcagtagtcacttct-----ctatgctt--aaatttgcagGTTGGTCTAAACAACATCAAGGAGACAGATTTTGTGAATGTCACAATACAGTCATTAATGAGAATTACTCCTTTAAGAAATTTCTTTCTCATCCCTGAAA
upper sequence: AT4G22350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 3
-------------------------------gtaatcc--tttctctttgattacacttgatcttgaaattaatgtctcctaaaggttaagcttgtaaatatgtagGTGGGGTTGAACAACATACAAAAGACAGAGTTTGTGAATGTTACAATCCAGTCGTTGATGAGAGTTACTCCTCTAAGGAATTTCTTCCTCATTCCTGAAA
||||| | | | | | | | ||| || ||| | || ||| | | |||| | || ||||||| | |||||||| | |||| || ||||||||||| ||||| ||||| || ||||||||||| ||||| || |||||||| || || |||||||
taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgccttttta-tctcatctataattgctgctt-----tgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacacttgatcttgaaattaatgtctcctaaaggttaagcttgtaaatatgtagGTGGGGTTGAACAACATACAAAAGACAGAGTTTGTGAATGTTACAATCCAGTCGTTGATGAGAGTTACTCCTCTAAGGAATTTCTTCCTCATTCCTGAAA
tcctaaa putative branch site (score: 2)
atcttgaaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcctttctctttgattacacttgatcttgaaattaatgtctcctaaaggttaagcttgtaaatatgtagGTGGGGTTGAACAACATACAAAAGACAGAGTTTGTGAATGTTACAATCCAGTCGTTGATGAGAGTTACTCCTCTAAGGAATTTCTTCCTCATTCCTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA