Sequence
atgc intronic sequence ATGC exonic sequenceGCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcattagaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43945.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G40350.2 (Glycine max), 5'ss of exon 3
GCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcattagaacttcatcctcttgtgtttga------ctccgatccatttaaaacatc-tctcgaataattcggtttcttgcag--------------------------------------------------------------------
|||||||| |||||| | |||||||| ||||| || | || ||||| |||||||| |||||||| |||||||| |||||||| || ||||||||||| |||||| | | || | || | || | | || | | | | |||| | | | | | ||| |||||
ACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCTATGCTATGGTTATAACTgtaagtttctgttattttactctatagtatcatatgctttcttgtagtcttgtggaacacaatatatggtgaattggtga--tgcagtatagttatgatttttgttaacaattccaatagctgtgtctcacaacttcttgtccatctgtttgtag
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv10s0042g00120.t01 (Vitis vinifera), 5'ss of exon 2
GCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcattagaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcag--------------------------------------------------------------------------------------------
|| |||| || ||| | |||||||||||||||||| |||||||||| ||| ||||||||||||| || ||||| || ||||| || ||||||||||| ||| | |||| |||||||| || | | ||| | | | |||| | || | | | || | |||
ACAAGAAGGGCCAAGAGCTATTGGCTTCTTTGGGACACGAAATATGGGATTCCTGCATCAAGAACTTATCGAGATCCTGAGCTATGCTATGGTTATAACTgtatgacattggaacttcagtctagtttatttta-tatgtaacattatgtgctcgtcaggcagaccagatgttttctcagtactggatcttaccactttcatgttggctgcatgggcgagcatatgttcctgattttcaaggtcattgctttaccgtaattttttcctgcag
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 4
GCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcattagaacttcatcc------tcttgtgtttgactccg-----atccatt-----taaaacatctctcgaataattcggtttcttgcag----------------------------------
|| ||||| || ||| | ||||| |||||||||||||| |||||||| |||| ||||||||||| |||||||| || ||||| || ||||||||||| ||| | | |||||| | | || ||| | || | ||| || | || | | | | |||| |
ACAACAAGGGCCAAGAGCTATTGGGTTCTTTGGGACAAGGAATATGGGATTCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTATGGTTATAACTgtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacag
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ38716 (Selaginella moellendorffii), 5'ss of exon 2
GCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcattagaacttcatcctct-tgtgtttgac--tccgatccatttaaaacatctctcgaataattcggtttcttgcag
|| ||||| || ||| | || |||||||| || || |||| ||||| |||||||||||| | || |||||||||||||| ||||| ||||| || || || ||| | | | | | || || | | ||| ||| | | |||| |||
ACAACAAGGGCCAAGAGCTATCGGCTTCTTCGGAACGCGAAACATGGGATTCATGCATCAACAGCTTATTGAGATACTTAGTTACGCGATGGTAATCACGgtgagtttcctgtttcgcgacgacgacgaagcagaaaatcgaaaggacgagaaaagtctaaccgtcggcttcacctcttccag
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ31428 (Selaginella moellendorffii), 5'ss of exon 2
GCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcattagaacttcatcctcttgtgtttgac---tccgatccatttaaaacatctctcgaataattcggtttcttgcag
|| ||||| || ||| | || |||||||| || || |||| ||||| |||||||||||| | || |||||||||||||| ||||| ||||| || || || ||| | | | | || | | ||| ||| | | |||| |||
ACAACAAGGGCCAAGAGCTATCGGCTTCTTCGGAACGCGAAACATGGGATTCATGCATCAACAGCTTATTGAGATACTTAGTTACGCGATGGTAATCACGgtgagtttcctgcttcgcgacgacgaagaagcagaatatcgaaaggacgagaaaagtctaaccgtcggcttcacctcttccagMapped 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|124812137|gb|EH897003.1|EH897003EST: TCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACC AAAAATCATATATACA
genomic: TCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcatt ... tttcttgcagAAAAATCATATATACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcattagaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC