Sequence
atgc intronic sequence ATGC exonic sequenceAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCAAGTTATGGCTGAAGgtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79830.3 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 5'ss of exon 5
AAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCAAGTTATGGCTGAAGgtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcag
||||| ||||||||| | || ||||| || || || ||||||||||| || || ||||||||||||||||||||||| || | ||| || ||||| ||||||| | |||| | || | ||| |||| || || | || | || ||| | | || || | || | || || | | | | |||||
AAAGAACGGGATACATTAAGGAGAGAGCAAAATAAAAAAAGTGATGCAGCTGCTCTTTTGAAAGAAAAGGATGAAATTATCAGTCAGGTCATGGCGGAAGgtataa-----------------tgaacca-acattttctttgtctc-ttctattatgattgcgtataaatgttaaatttgcaatacacaatgt--tcgttccgttgtaatgttgagacag------------------------
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G168654_T01 (Zea mays), 5'ss of exon 13
-------------AAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCAAGTTATGGCTGAAGgtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcag
|||||||| |||||||| || ||||||||||| || ||||||||||| || ||||||||||||||||||||||| || || ||||| || ||||||||||||| | | || || | || | | || || | || | || ||| |||| || | | | | ||| ||
ATATGCACTAACCAAAGAGCGTGATACACTAAGGAGAGAACAGAATAAAAAAAGTGATGCAGCTGCCCTTTTGAAAGAAAAGGATGAGATCATCAATCAGgtcatggctgaaggtatgtagaacctt--acatatt---atgcttggtc-tactatttttattgtaagccaatg---ttagattctcattattcaaagatctgtcccta-------------------------------------------------
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G43330.1 (Glycine max), 5'ss of exon 8
AAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCAAGTTATGGCTGAAGgtaagacagccttttggaatgcttgaat---tatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcag
|| || |||||||||| | |||| ||||| || ||||||||||| || || || ||||||||||||||||||||||| |||||||||||||| ||||||| || || | | | ||| ||| | ||| | | || | || || | || | | | | ||| | |
AAGGAAAGGGATACACTCCGCCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATCAAGTTATGGCAGAAGgtagtgcattctgaaatcaaacctaaatttgtatcatccaggctttgatggatacagaatcattttttttattaatgtctctttgggtttgattatatgg------------------------------------------------
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G01980.2 (Glycine max), 5'ss of exon 6
AAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCAAGTTATGGCTGAAGgtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcag
|| || |||||||||| | |||| ||||| || ||||||||||| || || || ||||||||||||||||||||||| |||||||||||||| ||||||| | || || ||| || || |||| | || | | | | | | | | | | || || ||| || | | | |
AAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATCAAGTTATGGCAGAAGgtagtgta---ttctgaaat---caaacctaaaattgtatcatcctggctttgatgga------tacagaattattttttttgttattaa----tgtctctttggggttgtttata-----------------------------
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv16s0098g00540.t01 (Vitis vinifera), 5'ss of exon 5
AAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCAAGTTATGGCTGAAGgtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcag
|| || |||||||||| |||||||||| | || |||||||||||||| ||||||||||||||||| ||||||||||| || |||||||||||||| ||| || | || || ||| | | || | || | | || || | || | | || | | ||||| || ||
AAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACCAAGTTATGGCTGAGGgtgagttgccaaaaaagacccaaaaaacccacaatcttttcttctcctttttgttttctttgtatttt-------cttctttatagtgca--tataacatttgtttgtc------------------------------------Mapped 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|164158478|gb|ES159755.1|ES159755EST: AATCAAGTTATGGCTGAAG GCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGC
genomic: AATCAAGTTATGGCTGAAGgtaagacagc ... atcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCAAGTTATGGCTGAAGgtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG