Sequence
atgc intronic sequence ATGC exonic sequencegtaatccttccattgagggttttagcctcgagtccttagctaattaattatgctcaatgacatatcataagcttggttaaaaggtgtaatgtagatattgctcttcttggttgcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04460.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G006965_T01 (Zea mays), 3'ss of exon 4
gtaatccttccattgagggttttagcctcgagtccttagctaattaattatgctcaatgacatatcataagcttggttaaaaggtgtaatgtagatattgctcttcttggttgcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT
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-----------atagtaggctaatgcactcaactcttcgatttatagtaagtttggggagtagcttatatgttatgt---gtggca-aaggctcatatttttcttttctgtc----cagGAATGGGAGGCTATCAATGATTTAAGAGCTGATATGGCTAGACTTCAGCAAGGCATGAGCCATATGCAAAGGATGTTGGAAGCTTGCATGGATATGCAGC
upper sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G081965_T01 (Zea mays), 3'ss of exon 4
gta-atcc--ttccattgagggttttagcctcgagtccttagctaattaattatgctcaatgacatatcataa---gcttggttaaaaggtgtaatgtag-atattgctcttcttggttgcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT
||| || | ||| || || | || | |||| | || | | | | ||| | | | | || ||| ||||| | || || |||||||||| | || || || |||||| ||| ||| ||||| |||||||| |||||| |||||||||||||| ||||| |||||||| ||||||
gtacatgcagatcctatgctatcttcacattcaataatggagcttttgtatagaaggagaaaaaactttttaactagtgcgttgagtcaaaaaaaagtaatatatttggttctgtgtttcttgcagGAATGGGATGCTATTAATGATTTAAGAGCTGACATGGGTAGACTTCAGCAAGGGATGAGCAGCATGCAGAGGATGCTGGAAGCGTGCATGGACATGCAGC
upper sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 7
gtaatccttccattgagggttttagcctcgagtccttagctaattaattatgctcaatgacatatcataagcttggttaaaaggtgtaatgtagatattgctcttcttggttgcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT
| || | ||||| | | | | || || || | || || || | ||| | || | || | ||| || | ||| | | || | | | |||| |||||| ||||||| || ||||| |||| |||||||||| |||||||| |||| || |||||||||||| | || |||||||||||||||||
----tttttattcctggagttttttctttg----cctaaatagttt-tcatactgtat--cttattaaaattctttttga----tgttctg---gttttgtt-tgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC
upper sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 6
gtaatccttccattgagggttttagcctcgagtccttagctaattaattatgctcaatgacatatcataagcttggttaaaaggtgtaatgtagatattgctcttcttggtt----gcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT
|||||| | | || || || || | | |||| || || |||||| | || || | | | | | ||| | | | |||| |||||| ||||||| || ||||| |||| |||||||||| |||||||| |||| || |||||||||||| | || |||||||||||||||||
------------------gttttattcctggagttttttct--ttgcctaaa-tagttttcatactgta--ttttattaaaattctttttgaagttctgggtttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcataagcttggttaaaaggtgtaatgtagatattgctcttcttggttgcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT
tagatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatccttccattgagggttttagcctcgagtccttagctaattaattatgctcaatgacatatcataagcttggttaaaaggtgtaatgtagatattgctcttcttggttgcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA