Sequence
atgc intronic sequence ATGC exonic sequencegtaccctaatcatttgcctctttctgaaaaaacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41060.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 4
----gtaccctaatcatttgcctctttctgaaaaaacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC
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gtaggtccaacattcattccaattcttatctcattgatgccgtaaccgcagttcagtagctaatccttt-acccatttttatt-tgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 4
-----------------gtaccctaat-catttgcctctttctgaa---aaaacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC
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gtaatcagtcctttttaaaatctttatatagtagtataatttaaaattaagtatctatcctactggacttgcaacttta--tatttg-tgtccattactgttacagACTACATATGAGAACTTCAGATACCGATATGATCGACGGGCCAACCCGTATAACACAGGAGTGTTCAATAATTTCTTAGAGATATTCTGCACCAGCATTC
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 4
----------------------gtaccctaatcatttgcctctttctgaaaaaacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC
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gtaatcattcctttttaaaatctttatatagtagtataatttaaagttaagctatctatcctacaggacttgcaacttta--tatttg-tgttcattactgttacagACTACATATGAGAACTTCAGATACCGATATGATCGACGGGCCAACCCGTATAACAAGGGAGTGTTCAATAATTTCTTAGAGATATTCTGCACCAGCATTC
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtaccctaatcatttgcctct--ttctgaaaaaacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC
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gtaacgggctcatcttcctaatgctatgattctgtagccgaaattttaggtcaaaatattgtgcctaacagcagaattt--tccttctctattccattcttttgcagACTACCTATGAGAATTTCAGATACCGATATGATCGACGAGCCAACCCCTACAACAAAGGAGTGGTGCAGAACTTCAAGGAGATATTTTGCACCAGCATTTMapped 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|164200289|gb|EL973085.1|EL973085EST: TCAGCACAAATCAG ACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACAT
genomic: TCAGCACAAATCAGgtaccctaat ... tattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC
tctttctttattctgt CT-rich tract
tttctttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccctaatcatttgcctctttctgaaaaaacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA