Sequence
atgc intronic sequence ATGC exonic sequencegtaaagatgttagtttgatatatatgctttttgaaatccatggctaggatccttggatgttaactttcttattgttcgtttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAGAAACTGCCTGAAGCAACAATCGGTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G26530.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G26530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------------gtaaag-atgttagtttgatatatatgctttttg--------aaatccatggctaggatccttggatgttaactttcttattgttcgtttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAGAAACTGCCTGAAGCAACAATCGGTGGAG
| || ||| | || | | || | | || | | ||| | || | |||| || ||| || ||||||||||||| ||||| ||||| | || |||||||||||||||| ||| | |||||||||||||||| |||||||
gtaaagttattaatcatttatttgtctttcatggttttaatattggaccatattaccatgacctacgaagcatgaactgggtttctgtgttgcagATTCCTGGTGTGCCAATTATGTACATCACCAGACCTACGAAGCATGAACTGGGTTTCTGTG---TTGCAGATTCCTGGTGTGCCAATTATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
upper sequence: AT1G26530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 8
gtaaagatgttagtttgatatatatgctt---tttgaaatccatggctaggatccttggatgttaactttcttattgttcgt-ttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAGAAACTGCCTGAAGCAACAATCGGTGGAG
|||||| ||| | | | || || ||| |||| | | ||| | || | | | | || | || ||| ||||||| ||||| ||||| ||||| | || |||||||||||||||| ||| | |||||||||||||||| |||||||
gtaaagtcattattcacttttccatctttggtttttaaatattggaccctgatgcatga---cccattatgtggttttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
upper sequence: AT1G26530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 8
gtaaagatgtt----agtttgatatatatgctttttgaaatccatggctaggatccttggatgttaactttcttattgttcgt-ttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAGAAACTGCCTGAAGCAACAATCGGTGGAG
|||||| || | ||| || | || || || ||| | | ||| | | | | ||| | | || ||| ||||||| ||||| ||||| ||||| | || ||||||||||||| || ||| | |||||||||||||||| |||||||
gtaaagtcattattcacttttccatctttgattgttttaatattggaccctgatgccagacccatga---tctgggtttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCGATTGAGCGATTGCCTGAAGCAACAATTGGTGGAGMapped 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|116464334|gb|EG506926.1|EG506926EST: GCTTCATAGTAGCTACTTGTGATAGAGTTCTAAAGCGAAGGATTCGCAAG ATTCCTGGTGTACCAATCATGTATGTGACCCAACGCAAGTACTCAATAGAG
genomic: GCTTCATAGTAGCTACTTGTGATAGAGATCTAAAGCGAAGGATTCGCAAGgtaaagatgt ... tcgtttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaaatccatggctaggatccttggatgttaactttcttattgttcgtttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAGAAACTGCCTGAAGCAACAATCGGTGGAG
tgttaac putative branch site (score: 2)
ctttcttattgttc CT-rich tract
ttaactttcttatt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagatgttagtttgatatatatgctttttgaaatccatggctaggatccttggatgttaactttcttattgttcgtttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAGAAACTGCCTGAAGCAACAATCGGTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG