Sequence
atgc intronic sequence ATGC exonic sequenceCTGCGACCATTATGGAACCATGCGTATCAAAGGCGGTAGCAATTATTCCTGCCGGTTGAAGTTCAAGGAGCAGTCAGTCATAGATCGAAACCCTCGTCAGgtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaatggaatttggtaatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13170.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 5'ss of exon 6
CTGCGACCATTATGGAACCATGCGTATCAAAGGCGGTAGCAATTATTCCTGCCGGTTGAAGTTCAAGGAGCAGTCAGTCATAGATCGAAACCCTCGTCAGgtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaatggaatt----tggtaatgcag----------------------------
|| || || |||||||||||||| ||||| ||| || | ||||| ||||| | ||||||||||||||||||| | ||||| ||||| || | ||||||| | | | | || | | | | |||||| | || || || || || | | |
TTGTGATCACTATGGAACCATGCGCATCAAGGGCAGTGGAAATTACTCCTGTAAGCTGAAGTTCAAGGAGCAGTCTATTATAGACCGAAATCCACATCAGgtact----ttgtgtgagttgaaatgaagaggataaaaagaacagactttctaaaacctttcccttgatatttctgagttttagagcttttttcctcctcttgt
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 5'ss of exon 7
CTGCG-ACCATTATGGAACCATGCGTATCAAAGGCGGTAGCAATTATTCCTGCCGGTTGAAGTTCAAGGAGCAGTCAGTCATAGATCGAAACCCTCGTCAGgtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaatggaatttggtaatgcag------------------------------
|| | | ||||| || |||||||| || |||| | || || ||||||||||||||||||||| | || ||||| ||||||| |||||| | || |||| | || | | | | || | | | | || | | ||
-TGTGGATCATTACGGTACCATGCGCATACAAGGTAACCGGGATCTCTCAATAAAATTGAAGTTCAAGGAGCAGTCAATAATTGATCGCAACCCTCATCAGgttctctaac--ttttcaactcaatttagcaattaaaattgaaggtcatgcgctaagacccagagattgtcaacggctagacttgtaatttctggattttag
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 5'ss of exon 7
CTGCGACCATTATGGAACCATGCGTATCAAAGGCGGTAGCAATTATTCCTGCCGGTTGAAGTTCAAGGAGCAGTCAGTCATAGATCGAAACCCTCGTCAGgtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaa---atggaatttggtaatg--cag---------------------------
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TGTTGATCATTACGGTACCATGCGCATCCAGGGCAACCGTCATCTTTCCATAAAATTGAAGTTCAAGGAGCAGTCAATAATTGATCGCAACCCTCATCAGgttctt---tacatcttaattcaatcct-ccgcaccttccaccgcctctttcacacgcagtactagttaacaattagactagttatttctgaattttagagcggMapped 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
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTGCGACCATTATGGAACCATGCGTATCAAAGGCGGTAGCAATTATTCCTGCCGGTTGAAGTTCAAGGAGCAGTCAGTCATAGATCGAAACCCTCGTCAGgtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaaatggaatttggtaatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG