Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgtagtttctttctctcctaaatttgatgaaactggctagtttgataacttgaaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04340.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------------gtaaatgtagtttctttctctcctaaatttgatgaaactggctagtttga---taacttg----aaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC
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gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 10
--------gtaaatgtagtttctttctctcctaaatttgatgaaactggctag---tttgataacttgaaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC
||| || || | | || || ||| ||| || | || | ||| || | |||||| |||||||||||||||||||| || ||||| || || || |||||||| |||||||||||| | || || || ||||| |||| ||| ||||||
aactaaaacgaaacagaggagtattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
-----------------gtaaatgtagtttctttctctcctaaatttgatgaaactggctagtttgataacttgaaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC
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atcagaaaacccccataatcagattaattatttgctgttatgccttt--ttattttcagttgtctagtaaattttaccttgag---gtattttttgataatg-cagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116432615|gb|EG475207.1|EG475207EST: CTTTTATCTTAGTCTTTTTCGCTCTTGCTTATGTCGTATACCGCCATCAG ATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCG
genomic: CTTTTATCTTAGTCTTTTTCGCTCTTGCTTATGTCGTATACCGCCATCAGgtaaatgtag ... ttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactggctagtttgataacttgaaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC
tgataac putative branch site (score: 2)
ccttctgtttatttgt putative PPT
tttatttgttttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgtagtttctttctctcctaaatttgatgaaactggctagtttgataacttgaaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA