Sequence
atgc intronic sequence ATGC exonic sequenceTCAAGATTTTGGAGCATTTGAGGAGTTTGGGCTGTGGTGCTGTGTTGGTTAGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattctttatccccaataataaagtttgaatatttttttatttggtctcatgttgatgtgtagtttttgaccatgtcttcggtgtggatgaaatgaatag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11880.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA03G33830.1 (Glycine max), 5'ss of exon 1
TCAAGATTTTGGAGCATTTGAGGAGTTTGGGCTGTGGTGCTGTGTTGGTTAGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattctttatccccaataataaagt------ttgaatatttttttatttg-gtctcatgttgatgtgtagtttttgaccatgtcttcggtgtggatgaaatgaatag-----------------
| ||||||||||| ||||||||| ||||| |||||||||||| | |||||||| |||||||| ||| | ||||||| |||||| || |||||||| | || | | | | ||| || || | ||| | |||| | || ||| ||| | || |||||| | | || | | || | ||||
TGAAGATTTTGGAACATTTGAGGCACTTGGGTTGTGGTGCTGTGCTTGTTAGTGGGAATGAGCTTAGGTTGGCTCTTCGTGCTGGCTTTGATCCCACGAGgtttaacaatct-cactcaaccatgaatttgttttttgtgttcttttccacccacgttgcatattgttttgctgtttttttttttttttttgtattttctgttgttaataattttatgtgattcttag
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G06090.2 (Glycine max), 5'ss of exon 2
TCAAGATTTTGGAGCATTTGAGGAGTTTGGGCTGTGGTGCTGTGTTGGTTAGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattctttatccccaataataaagtttgaatatttt--tttatttg-gtctcatgttgatgtgtagtttttgaccatgtcttcggtgtggatgaaatgaatag
||| |||||||||||||| |||||||||||||||||| | |||||||| |||||| | || | ||||||| |||||| || |||||||||| || ||| | || | | || | || | | | |||||| || | | ||| | | | | | | | || | | || |
-----ATTCTGGAGCATTTGAGGCAGTTGGGCTGTGGTGCTGTGCTTGTTAGTGGGAATGAGTTTAGTTTGGCTCTTCATGCTGGGTTTGATCCCACAAGgttgaatttcacttaacccttgagtgtgtctacatgtatcaatctatttgtgtttttttaagatcctttatgcacggct-tattataggagcgtatcctgt------
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G36580.1 (Glycine max), 5'ss of exon 1
TCAAGATTTTGGAGCATTTGAGGAGTTTGGGCTGTGGTGCTGTGTTGGTTAGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattctttatccccaataataaagt------ttgaatatttttttatttg-gtctcatgttgatgtgtagtttttgaccatgtcttcggtgtggat-----gaaatgaatag------------------------
| ||||||||||| ||||||||| ||||| |||||||||||| | |||||||| |||||||| | | | ||||||| ||||| || |||||||||| || || | | | | | || || | ||| | ||||| | || | ||||||| | | ||||||| | | | | |||| | || ||
TGAAGATTTTGGAACATTTGAGGCACTTGGGTTGTGGTGCTGTGCTTGTTAGTGGGAATGAGCTGAAGTTGGCTCTTCGAGCTGGCTTTGATCCCACAAGgtttaataatgtcactcaacccatgaatttgtttgttgtgttctttttcacctgcattgcatgttgtttggctgtttttgtattttgtgttgttaaggattttttgtgattcttaatgtaattttgggttggatgaatag
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA13G20390.1 (Glycine max), 5'ss of exon 2
TCAAGATTTTGGAGCATTTGAGGAGTTTGGGCTGTGGTGCTGTGTTGGTTAGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattctttatccccaataataaagtttgaatatttttttatttggtctcatgttgatgtgtagtttttgac-catgtcttcggtgtggatgaaatgaatag
| |||||| |||||||||||||| ||||| |||||||||||| | || ||||| |||||||| || | ||||||| ||||| || ||||| |||| || ||| | | || | | || || | | | || | || | | | | || | | || | | | | |
TGAAGATTCTGGAGCATTTGAGGCAGTTGGGTTGTGGTGCTGTGCTTGTGAGTGGGAATGAGCTTAGATTGGCTCTTCGGGCTGGGTTTGATCCGACAAGgttgaatt----acacttaacccttggatgtgtctacatgtatcaatgtatttgtggttttttaagatcctttatgcgcagctattataggaacatatcctgtg-
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ12224 (Selaginella moellendorffii), 5'ss of exon 1
TCAAGATTTTGGAGCATTTGAGGAGTTTGGGCTGTGGTGCTGTGTTGGTTAGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattctttatccccaataataaagtttgaatatttttttatttggtctcatgttgatgtgtagtttttgaccatgtcttcggtgtggatgaaatgaatag
| || || | |||||||| |||| |||||| ||||||||||| | || |||||||||||||| |||||||| | | |||||| || |||||||| | ||| || ||||| | | || || | | | || | | | ||||| | ||
TGAAAATCCTCGAGCATTTCCGGAGCTTGGGCAGTGGTGCTGTGCTCGTCAGTGGAAATGAGCTTAGGCTTGCATTGCATGCTGGCTTTGATCCCACCAGgtaaagttttttattttctttttc---cttccaagacatactcgagga-----ataactcttttttttttttcatcag--------------------------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|47831454|gb|CK121138.1|CK121138EST: AGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAA GTGTATTTTCAATGGAAATGGAAAGTCTTTGGAAGATTTAGTTCTAGCTGC
genomic: AGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattct ... aaatgaatagGTGTATTTTCAATGGAAATGGAAAGTCTTTGGAAGATTTAGTTCTAGCTGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCAAGATTTTGGAGCATTTGAGGAGTTTGGGCTGTGGTGCTGTGTTGGTTAGTGGAAATGAGCTCAGGCTTGCTCTTCTTGCTGGTTTCGATCCCACAAAgtacgattctttatccccaataataaagtttgaatatttttttatttggtctcatgttgatgtgtagtttttgaccatgtcttcggtgtggatgaaatgaatag
- - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA