Sequence
atgc intronic sequence ATGC exonic sequencegtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaatggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 6
------------gtagtagaatgatttttatttctgtctttctgctcgtatgaaca--------ggcct------ttaaatgg---aatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
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gcatatcaatatctagtagtctgttttgtggttttataaacatattaat-tggacactgttcccagcctcccacattaaatagtttgaattgctcgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAGAAAGTTGCTATGTTAATCGGAAAATGGGATGAAGCTATGTATTATGTTCTTGGGGATCCAAGTG
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
---------------------------gtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaa-atggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
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ggttaagttagcagcagtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattgttctaatcatttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 6
----------------gtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaa------------tggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
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aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacatttataagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 6
--------------------gtagtagaatg-atttttatttctgtctttct-gctc---gtatgaacaggcctttaaa---tggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
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agaaatttggcaattccaaatgagtagtttggattcgtctatccgcttttcttgttctgagttttatgagactgaaagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
-----------------gtagtagaatgattttt--atttctgtctttctgctcgta----tgaacaggcctttaaatggaatttggtaa-----tgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
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caaacggtgctatcactctgaatcgatgctttttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAAMapped 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|124806174|gb|EH893153.1|EH893153EST: ATAGATCGAAACCCTCGTCAG GTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTG
genomic: ATAGATCGAAACCCTCGTCAGgtagtagaat ... ggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctgtctttctgctcgtatgaacaggcctttaaatggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
tttaaatggaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaatggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC