Sequence
atgc intronic sequence ATGC exonic sequencegtaagaagttatcgagcttttactcttttaattttggatatgaggtgtgtggcctaataaggtatttttcttatggtttgtttggtaagATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAGATACAATGGGTAATGTCGATATATTCGTTGCCGGAATAGGAACTGGTGGTACTGTAACTGGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03630.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G00900.1 (Glycine max), 3'ss of exon 4
-----------------------------------gtaagaagtta-----tcgagcttttactcttttaattttggatatgaggtgtgtggcctaataaggtat-ttttcttatggtttgtttgg------ta-agATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAGATACAATGGGTAATGTCGATATATTCGTTGCCGGAATAGGAACTGGTGGTACTGTAACTGGTA
||| | | | | || | || || | | | || | | | | ||| || | || ||| | ||| | || || |||||||||| ||||||||||| ||||| || ||||| ||||| ||||||||||| || ||||| || || || || ||||||||||| ||||| ||||| |
gttaagtcttaatgcatctcccataagaccttcacttaatcaatcactgttttgaattatttatcgcatcaatgaaactagaaactataaaataaattaatttacatgttattaagatttatatgcacaaattacagATCCACTTCGAAACTACAGGGCCAGAGATATGGGAGGATACCATGGGTAATGTTGACATATTGGTAGCTGGGATTGGAACTGGTGGCACTGTTACTGGCA
upper sequence: AT3G03630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G29740.1 (Glycine max), 3'ss of exon 4
--------------------------------------gtaagaagttatcgagcttttactcttttaattttggatatgaggtgtgtggcctaa--taaggtat-ttttcttatggtttgtttgg------ta-agATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAGATACAATGGGTAATGTCGATATATTCGTTGCCGGAATAGGAACTGGTGGTACTGTAACTGGTA
| | | | | || | | | ||| | || || ||| |||| || | || ||| | || | || || |||||||||| ||||||||||| ||||| || ||||| ||||| ||||||||||| ||| |||| || || || || ||||||||||| || || ||||| |
gttaagtctcaatgcatctcctataagaccttcaccttatcaatcactgttttgaattatttagtgcatcattgaaaatagaaattgcaatataaattaagttacatgttattaagacttatatgcacaaattacagATCCACTTCGAAACTACAGGGCCAGAGATATGGGAGGATACCATGGGTAATGTTGATGTATTGGTAGCTGGGATTGGAACTGGTGGCACCGTTACTGGCA
upper sequence: AT3G03630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0056g00820.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaagttatcgagcttttactcttttaattttggatatgaggtgtgtggcctaataaggtatttttcttatggtttgtttggtaagATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAGATACAATGGGTAATGTCGATATATTCGTTGCCGGAATAGGAACTGGTGGTACTGTAACTGGTA
| ||| || | | || || || | | | | | | ||| || | | | || | || | | |||| ||||||||||||||||| |||||||| ||||| ||||| |||||| ||| || ||||| ||||| ||||| || |||||||||||||| || || |
-------------gttgtttctgtcatctcatgccagacataaagcctttttctttatattctaaatatatgattttgtggatt-tcagATACACTTTGAAACTACAGGTCCAGAAATATGGGAGGATACTGTGGGTAGTGTTGACATATTTGTTGCTGGAATTGGGACTGGTGGTACTGTTACAGGCAMapped 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|164081308|gb|ES064427.1|ES064427EST: CAAAGAACGCATATATGTTTCAGCAATTCGACAATACAGCAAATACAAAG ATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAG
genomic: CAAAGAACGCATATATGTTTCAGCAATTCGACAATACAGCAAATACAAAGgtaagaagtt ... gtttggtaagATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatatgaggtgtgtggcctaataaggtatttttcttatggtttgtttggtaagATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAGATACAATGGGTAATGTCGATATATTCGTTGCCGGAATAGGAACTGGTGGTACTGTAACTGGTA
gcctaat putative branch site (score: 3)
tttgttt putative PPT
taataaggtattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaagttatcgagcttttactcttttaattttggatatgaggtgtgtggcctaataaggtatttttcttatggtttgtttggtaagATCCACTTTGAAACTACAGGACCAGAAATCTGGGAAGATACAATGGGTAATGTCGATATATTCGTTGCCGGAATAGGAACTGGTGGTACTGTAACTGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG