Sequence
atgc intronic sequence ATGC exonic sequencegtactagtatataaagctatatcatccattttcctcatgctcattgtttatgtcactataattaacaacttaaaaatttcccctttctcacttttttaattggttttcatattaacttgctagAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGTGCATATTGGGGACTAACCACACTGGCTTTACTCGACAAGCTTGGTTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G11710.1 (Glycine max), 3'ss of exon 2
gtactagtatataaagctatatcatccattttcctcatgctcattgtttatgtcactataattaacaacttaaaaatttcccctttctcacttttttaattggttttcatatta-acttgctagAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGTGCATATTGGGGACTAACCACACTGGCTTTACTCGACAAGCTTGGTTCTG
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------------gtgggtgtgcttcccattt-----atatatat-atatacatacatacatacattctttctcaaaactcttctttaatgctt----aaaaggttgtccttttatggtttccagAGGAAAGATAACTTTGAATCTGTAGTAATGGAGCATCTGAGAATGAATGGGGCATACTGGGGATTGACCACTCTGGATCTTCTAGGAAAGCTTCATTCTG
upper sequence: AT3G12070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G28630.1 (Glycine max), 3'ss of exon 1
gtactagtatataaagctatatcatccattttcctcatgctcattgtttatgtcactataattaacaacttaaaaatttcccctttctcacttttttaattggttttcatattaacttgctagAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGTGCATATTGGGGACTAACCACACTGGCTTTACTCGACAAGCTTGGTTCTG
| |||| ||||| || | ||| ||| | ||| | | | || || | | | | | | || | ||| ||||| | ||||| ||||| || ||||| ||||| ||||||||||| |||||||||||| | ||||| |||| | | || | |||||| | | |
-----------------------------gtgtgctgtgcttcccatttatac-------atggatgccttgcaaact----cttctttaatgcttaaaaggttgtccttttatggtttccagAGGAAAGATAACTTTGAATCTGTCGTAATGGAGCATCTAAGAATGAATGGGGCATATTGGGGATTGACCACTCTGGATCTTCTAGGAAAGCTTCATACCG
upper sequence: AT3G12070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0024g00080.t01 (Vitis vinifera), 3'ss of exon 2
gtactagtatataaagctatatcatccattttcctcatgctcattgtttatgtcactataattaacaacttaaaaatttcccctttctcacttttttaattggttttcatattaacttgct------agAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGTGCATATTGGGGACTAACCACACTGGCTTTACTCGACAAGCTTGGTTCTG
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------------------------------------gtgcgttttgttt-tatta--gcaatcaattattcttttcttttttggtcatgccatatttagttgaatttcagatgattttgttgtactcagAGGAAGGACAATTTTGAATCAGTGGTGATGGAACATCTAAGAATGAATGGGGCATACTGGGGACTGACTACTCTAGATCTTCTAGGAAAGCTGGACATGGMapped 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|86024985|gb|DR320738.1|DR320738EST: TCGTAGCTGACAAGCATCTTCGTTACATTCTGAATTTGATGGCAGAAAAG AAAAAAGAGAGTTTTGAGTCTGTGGTGATGGATCATCTGAGAATGAATGGT
genomic: TCGTAGCTGGCAAGCATCTTCGTTACATTCTGAATTTGATGGCAGAAAAGgtactagtat ... aacttgctagAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGT
EST:
gi|86024984|gb|DR320737.1|DR320737EST: TCGTAGCTGACAAGCATCTTCGTTACATTCTGAATTTGATGGCAGAAAAG AAAAAAGAGAGTTTTGAGTCTGTGGTGATGGATCATCTGAGAATGAATGGT
genomic: TCGTAGCTGGCAAGCATCTTCGTTACATTCTGAATTTGATGGCAGAAAAGgtactagtat ... aacttgctagAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaaaaatttcccctttctcacttttttaattggttttcatattaacttgctagAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGTGCATATTGGGGACTAACCACACTGGCTTTACTCGACAAGCTTGGTTCTG
tattaac putative branch site (score: 1)
ttttttaattggtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactagtatataaagctatatcatccattttcctcatgctcattgtttatgtcactataattaacaacttaaaaatttcccctttctcacttttttaattggttttcatattaacttgctagAAAAAAGAGAGTTTTGAGTCTGTGGTTATGGATCATCTGAGAATGAATGGTGCATATTGGGGACTAACCACACTGGCTTTACTCGACAAGCTTGGTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT