Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttgaatatacttgagatggtgaacttataatgaaggctgctcttttaatttttgccaccttacctcaagcaattattggtctggattttctgcatcacttcagcctttatttgtgcagATGATCCAGCATTGATCGTCTACACTAGTGGTACAACTGGTAAGCCAAAAGGAGTTGTTCATACTCACAACAGCATCAATTCCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16170.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G02180.2 (Glycine max), 3'ss of exon 4
gtaagtttttgaatatacttgagatggtgaacttataatgaaggctgctcttttaatttttgccaccttacctcaagcaattattggtctggattttctgcatcacttcagcctttatttgtgcagATGATCCAGCATTGATCGTCTACACTAGTGGTACAACTGGTAAGCCAAAAGGAGTTGTTCATACTCACAACAGCATCAATTCCCAG
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----------gtaagaaaatcagtttcagtttttataaacagagtgggt--tgaattttttgctagcaatttgttgacagttagttctttg--tttttcatatccattcg-----catagGTGAAGAT---CCAGCACTGATTTTGTACACTAGTGGGACAACGGGTAAACCTAAGGGAGTTGTTCATACACACAGAAGCATCATTTCCCAG
upper sequence: AT3G16170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G21840.1 (Glycine max), 3'ss of exon 4
gtaagtttttgaatatacttgagatggtgaacttataatgaaggctgctcttttaatttttgccaccttacctcaagcaattattggtctggattttctgcatcacttcagcctttatttgtgcagATGATCCAGCATTGATCGTCTACACTAGTGGTACAACTGGTAAGCCAAAAGGAGTTGTTCATACTCACAACAGCATCAATTCCCAG
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----------gtaagaaaatcagtttcagtttttataaatggataggttgactt---ttttgttcgcaagttttagacagttagttctttg--ttttcaactccattcg------catagGTGAAGAT---CCAGCACTGATTTTGTACACTAGTGGGACTACAGGTAAACCTAAGGGAGTTGTTCATACACACAAAAGCATCATTTCCCAG
upper sequence: AT3G16170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g04170.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtttttgaatatacttgagatggtgaacttataatgaaggctgctcttttaatttt-tgccaccttacctcaagc-aatta--ttggtctggattttctgcatcacttcagcctttatttgtgcagATGA---TCCAGCATTGATCGTCTACACTAGTGGTACAACTGGTAAGCCAAAAGGAGTTGTTCATACTCACAACAGCATCAATTCCCAG
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----------------------gtaagtggaataa-attagaaggtgttttacaaaccttatgataacaccctttaagttaatcaacttctttttttcttttaataattttttatttcccaatggtgcagATGAGGATCCTGCTCTCATTATATACACTAGTGGTACAACAGGGAAACCTAAAGGAGTTGTTCACACACACAAAAGCATTAATTCACAGMapped 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|163972925|gb|ES197017.1|ES197017EST: TTGCAATCAGTTTCAGGATGACAGTTTTGAAGCAGAAGGAAAGTTTCTAG ATGATCCAGCATTGATCGTCTAACACTAGTGGTACAACTGGTAAGCC
genomic: TTGCAATCAGTTTCAGGATGACAGTTTTGAAGCAGAAGGAAAGTTTCTAGgtaagttttt ... atttgtgcagATGATCCAGCATTGATCGTCTA-CACTAGTGGTACAACTGGTAAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcaagcaattattggtctggattttctgcatcacttcagcctttatttgtgcagATGATCCAGCATTGATCGTCTACACTAGTGGTACAACTGGTAAGCCAAAAGGAGTTGTTCATACTCACAACAGCATCAATTCCCAG
cctttattt CT-rich tract
tttatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttgaatatacttgagatggtgaacttataatgaaggctgctcttttaatttttgccaccttacctcaagcaattattggtctggattttctgcatcacttcagcctttatttgtgcagATGATCCAGCATTGATCGTCTACACTAGTGGTACAACTGGTAAGCCAAAAGGAGTTGTTCATACTCACAACAGCATCAATTCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG