Sequence
atgc intronic sequence ATGC exonic sequenceGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53620.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 6
GTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag
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GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAGTCGGGGCTTATCAAGgttgtaat--agttgc-tgagttattttcgat---tctacggttactaa--gtcaagttg-ctaaacacta-atctatgcacag
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 6
GTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag
||| ||||||| || |||||||||||||||||||||||||| ||||||| ||||||| || ||||| ||| ||||| || || | | || | ||| | || | | |||| || | |||
GTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAATCGGGTCTTATCAAGgttgcaatc--gttgcagagttattttttattatattgtt-actatgtcaagttctaaacactaatctatgaacag--------
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 4
GTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag
||||| || ||||| ||||| |||||||||||||||||||| ||||||| || || || |||| |||| | || |||| || |||| | || || | | | || | | ||| | | | || ||| |||
GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgta--atcatggttgc-ctagcttttt---cttcccttgttacacttgttgacaggatattgctgaacatgcatctatgtgcag
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G05130.1 (Glycine max), 5'ss of exon 4
GTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag
|||||||| || || ||||| || ||||||||||||||||| ||||||| || ||||| |||| |||| || | | || | | |||| | | || || ||| |||| || ||| || ||| |||
GTGGTTGAAATTGGGAAAGGAAGTAAGGTGAAATATGAACTTGACAAAAGAACTGGTCTTATTATGgtaatcatcgctgcctagttttttcttcccttgtcgcacttgttgctacaggat--attg-ctgaacag-gcatctatgtgcag
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 4
GTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag
|||||||| ||||| |||||||||||||||||||||||||| ||||| | || || || || |||||| | || | || | ||| | | | | || || || | | | ||| ||||| |||| | || |||
GTGGTTGAAATAGGGAAAGGGAGCAAGGTGAAATATGAACTTGACAAGAAAACTGGACTGATCAAGgtaattaggtgttctaatccatttttctaggtactctttgcag-atcaacaat-tggttg-ctaaattttatattcatgtgcagMapped 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|164122543|gb|ES019056.1|ES019056EST: AGGGAGCAAGGTGAAATAATGAACTCGACAAAACTACGGGTCTCATTAAG GTCGACCGTATTCTTTACTCATCTGTCGTTATACCCACACAACTATGGGTT
genomic: AGGGAGCAAGGTGAAAT-ATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaattt ... atattctcagGTCGACCGTATTCTTTACTCATCTGTCGT-ATACCCACACAACTATGGGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag
- - - - - - - - - GGAGCA
- - - - - - - - - - AGCAAG