Sequence
atgc intronic sequence ATGC exonic sequenceGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaatgacatactgttaagataggaagtttttgtttgcttctggatatttaaggtgtaaagctgata...
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51690.3 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaact-tcatctatt--tcgtttgtttgcctctgaatgacatactgttaagataggaagtttttgtttgcttctggatatttaaggtgtaaagctgata
||| || || ||||| |||||||| || | ||||| ||||||||||||||||| | ||||| || || || |||||||| || || |||||||||||||| | |||| || || | | || || || || ||| | | || ||| | | || || | || | | | ||
GGAAATTGAAGAGAAGATTAACAAGATAAAGTGGTGCCAAACAGCAAATGGAGCATTGTTTCTTCTGTCCACAAATGATAAGACAATAAAGTTTTGGAAGgtattattcatcatttagaaatcatagaaatttcttgtaaaccagtattgctaaactgttgcatgcttctttacatatgtatgtgcaa--ctcagtgataat-
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G20830.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaatgacatactgttaagataggaagtttttgtt--tgcttctggatatttaaggtgtaaagctgata--
||| ||||| ||||||||||||||||| | |||||| |||||||| ||||| ||| | || || || || || ||||||||||||||||| ||||||||||| || | || | || |||| | ||||||| || | ||| | | | | | | ||| || | ||| | || |
GGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAGgtatgaaatgaat---tctcacttgtgggatgctgaatgctatttttttattcaatttatatatgaatgacacacatggttacatttc-tgtcgaactaagttt
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaatgacatactgttaagataggaagtttttgtttgcttc---tggatatttaaggtgtaaagctgata
||| ||||| ||||||||||||||||| | |||||| |||||||| ||||| ||| | || || || || || ||||||||||||||||| ||||||||||| || | || || |||| | ||||||| || | || | | | | || || | ||| || | ||| |
GGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAGgtatgaaatgaatgc---tcacttgtgggatgctgaatgctattttttttattcaatttatatatgaatgacacacatggttacatttctgtcaaaataagtt
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaa--tgacatactgttaag--ataggaagtttttgtttgcttctggatatttaaggtgtaaagctgata
|||||| || |||||||| |||||||| |||||||| |||||||| ||||| || || || || || || || ||||||||||| ||||| ||||||||||| || | || | || | || | || ||| | | || || | | || || | || | | | ||| ||| |
GGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATAAAACGATCAAATTTTGGAAGgtatgaaatgaatgatcacctttagcatgttttcagtgctgtcat-ttatcaattcattgataaattgtgcacaagtttgcacttctgaggaactaagttt---
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaa--tgacatactgttaag--ataggaagtttttgtttgcttctggatatttaaggtgtaaagctgata
||| || || |||||||| |||||||| |||||||| |||| ||| ||||| || || || || || || || ||||||||||| ||||| ||||||||||| || | || | || | ||| | | || ||| | | || || | | || || || | | | ||| ||| |
GGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATAAAACAATCAAATTTTGGAAGgtatgaaatgaatgatcacctttagcatgcttttagtgctgtcat-ttatcaattcattgataaattgtgcacaaggttgcacttctgaggaactaagttt---
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgt------gaaaacttcatctatttcgtttgtttgcctctgaatgacatactgttaagataggaagttt----ttgtttgcttc----tggatatttaaggtgtaaagctgata--------------------------------------------------
||| |||||||||||||| || || || |||||||| || ||||||||||| || || ||||| || || || |||||||||||||| |||||||||||||| | ||| || ||| || |||| | | |||| | | | | | | | || | ||| | || | | | | |||
GGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATAAAACCATTAAGTTTTGGAAGgtaggaagggaaaattgtcttatgaaactttaaacttcctgatttttaatttgttgacagattatgctcaacatcaccaactccagtttggtttctttaactactgatataatatatatcctgcacatgctgattacatagctgtcttttcgagaatgaaacag
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ08844 (Selaginella moellendorffii), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaatgacatactgttaa-gataggaagtttttgtttgcttctggatatttaaggtgtaaagctgata
|||||||||||| || || |||||||| ||||||||||| || || || || |||| |||| | | || || ||||| || ||||||||| |||||||||| | | || | | || | || | ||| || | || | | ||
GGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACAAGACCATCAAGCTTTGGAAGgtaggatttctattcggattaacttgacgcgtatg--ttgcatcctatgaacaacgagcag----------------------------------------
upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ09063 (Selaginella moellendorffii), 5'ss of exon 4
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaatgacatactgttaagataggaagtttttgtttgcttctggatatttaaggtgtaaagctgata
|||||||||||| || || |||||||| ||||||||||| || || || || |||| |||| | | || || ||||| || ||||||||| |||||||||| | | || | | || | || || ||| | | | ||
GGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACAAGACCATCAAGCTTTGGAAGgtaggatttctattcggattaacttgacgcgtatgttggatcctctga-acaacgagcag----------------------------------------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|86070772|gb|DR366529.1|DR366529EST: ACCATCAAGTTTTGGAAG GTTCAAGACAAGAAGATCAAGAAAATCTGTGATATGAATTCAGATCCTTCA
genomic: ACCATCAAGTTTTGGAAGgtgaaaactt ... gtcttaacagGTTCAAGACAAGAAGATCAAGAAAATCTGTGATATGAATTCAGATCCTTCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATAAAACCATCAAGTTTTGGAAGgtgaaaacttcatctatttcgtttgtttgcctctgaatgacatactgttaagataggaagtttttgtttgcttctggatatttaaggtgtaaagctgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG