Sequence
atgc intronic sequence ATGC exonic sequencegtaagatatgtgtttatggttttttctcatgactcaatatactgtcaattttgtttgttttcgggaacaagcatgttctaaagcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16143.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 4
gtaagatatgtgtttatggttttttctcatgactcaatatactgtcaattttgtttgttttcgggaacaagcatgttctaaagcttgtttgtttcttaatcttttcat-----gtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG
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gtatccgatcatctcctgacttgtctttgtg-ctttctgtacttcc--ttgatattatttt---gattgagtgcattgttggagttattaatgtttttacctcttgaaaaaaaattgaagGCTGTATGGGCATTGGGCAATGTTGCTGGTGATTCCCCTAAGTGCCGTGACCTTGTTCTTGCCAATGGTGCATTGCTGCCTCTGCTAGCACAGTTGAATG
upper sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 4
gtaagatatgtgtttatggttttttctcatgactcaatatactgtcaattttgtttgtt-ttcgggaacaagc-atgttctaaagcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG
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---------gtatttat---tcagtcttttggctttct-tgct-----ttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG
upper sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 4
gtaagatatgtgtttatggttttttctcatgactcaatatactgtcaattttgtttgttttcgggaacaagcatgttctaaagcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG
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-----gtatttatttagtcttatcttttgtgctttcttat--tttctatttaggagtgtatgatgtgtgacagtgccct-----ttctctgttttaaaaca-----atacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG
upper sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S230_50V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagatatgtgtttatggttttttctcatgactcaatatactgt-caattttgtttgttttcgggaacaagcatgttctaaa-gcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG
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-----tgatgtaatgaagg-------taatgatactaagtgctattcactcctgagtttcttcaataatgactgtcttcttactgagaacccgtgtcaccttgtttttgc-----agGCTGTATGGGCATTAGGGAATGTAGCGGGTGACTCTCCAAAGTGCAGAGATCTTGTTCTTAACCATGGCGCTTTGATGCCTCTGCTTGCTCAGCTTACTGMapped 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|116411698|gb|EG454290.1|EG454290EST: CGATTTTTGTTCAACTATTGGCTTCTCAGAGTGATGATGTCCGTGAGCAG GCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGAT
genomic: CGATTTTTGTTCAACTATTGGCTTCTCAGAGTGATGATGTCCGTGAGCAGgtaagatatg ... catgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgggaacaagcatgttctaaagcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG
tttcttaatcttttc CT-rich tract
tttcttaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatatgtgtttatggttttttctcatgactcaatatactgtcaattttgtttgttttcgggaacaagcatgttctaaagcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT