Sequence
atgc intronic sequence ATGC exonic sequenceGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.2 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 12
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaatta---attatgtgttgtttgtttacag----------------------------
||| || ||||| || ||||||| || |||||||| ||||| ||||||||||| |||||||||||||| ||||| ||||||||||||||| | | |||| ||| | || | | || ||||| | || | ||| | | ||| |||| |
GAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAGgtt-----ttatttaatttattttaagatttaaaaacactg----gtttagcactaagcaatatcttctatttatttatataacagaatatgcttcatattctatgcag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 12
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtt--tgtttacag--------------------
|||||||||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||||| | ||| |||| ||| | || | || || | | | | ||
GAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAGgtttacaattttgtaccttattatttgttattctgttcatcatagttaggcttctatctagaaatcactaatactagcactggacacagttataagatgt
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 12
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttgg---tctc---ctctccgtgaatttcaagttaa--aacagccatgagaggtttaaaat-taattatgtgttgtttgtttacag--------
|||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| || ||||||||| | | | || | | |||||| | || | | || | | ||| || | || || | | ||| |
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAGgtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 12
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtc-tcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacag---------------------
|||||| ||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||||| | | | | | | | | |||| ||| | ||| | || | | || | ||
GAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAGgtttacaattttgtactttattattttgttattctgttcatcattagttatgcttctatctagaaatcactgatactagcactggacagttataagatgt
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 12
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgtt---ggtctc---ctctccgtgaatttcaagttaa--aacagccatgagaggtttaaaattaattatgtgttgtttgtttacag--------
|||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || || || || ||||||||| | | || | | | ||| | || | | || | | | | | | || |||| ||| |
GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAGgtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgta-atttgtaatggtacag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 12
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacag------------
|||||| ||||| || |||||||| || |||||||| ||| ||||||||||||| ||||||||||||||||||||||||||||| |||||| | | | ||| ||| |||| | | | | | | | ||| | | || || ||| |
GAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAGgttcattttgttcttgtg--ttttgcattaagctatcta--aagatatcatatataaatgcttatttcttctttctgggttaattatcag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 12
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacag
||| || |||||||| |||||||| || ||||| || ||| ||||||| || ||||||||||||||||| || ||||| ||||| |||| ||| || |||| | ||| |||| || | |
GAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAGgtaaaagg-------atgacttgtgtgttatttctttgctgactcgttttctgtttctcag-----------------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|116473628|gb|EG516220.1|EG516220EST: ATAGGATTGGTCNNNNNNNNGAAGTTCAAGTGTTTCGATTCTGCACTGAG TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTT
genomic: ATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcc ... ttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT