Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatttgttgtgtttcagcttcagaggttctttccatataatggatggcttacatgtatattctcttgcttgtgtttcttagCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23670.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 6
--------gtaagcatttgt-tgtgtttcagct--tcagaggttctttccata---taatggatggcttacatgtatattctcttgcttgtgtttct-tagCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
| |||||| | | ||| | | | || ||| | || | | | || ||| | | | | ||||| || | | || || ||| || ||| | ||| ||| ||||||||||||||||| || || ||||||||||||||| | || |||||||| || || ||| |||| || || ||
gtatttttttttcaatttgtctctatttgtgttaatatgatgttgctcacagaggttgcagtattatttat-tctctttcttcttggttatttacctacagAGCCATCTCATCTAGAAGAAGTGTTGAGAGAACAAATTGCTGAGGGACAACCTAGGACACATAGGCCTTGGAAGAAGATAATGGTTATTGTGGAGGGGAT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 6
--------gtaagcatttgttgtgtttcagcttca---gaggttctttccatataatg-gatggcttacatgtatattct-cttgcttgtgtttct-tagCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
| ||||||| || || | || ||| | || | || | | || | |||| |||| | | | || || ||| || ||| | ||| ||| || |||||||||||||| || || ||||||||||||||| | || |||||||| || || |||||||| || || ||
ttgcatttttttcaatttgtttctatttgtgttaatatgatgttgctcacagaggttgcagtattatttattcactttcttcttggctatttacctacagAGCCATCTCATCTAGAAGAAGTGTTAAGAGAACAAATTGCTGAGGGACAACCTAGGACACATAGGCCTTGGAAGAAGATAATGGTTGTTGTGGAGGGGAT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcatttgttgtgtttcagcttcagaggttctttc-----------catataatggatggcttacatgtatattctcttgc-ttgtgtttctta--gCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
||| | | ||| ||| || | || || |||| | | || | | ||| |||| | | | | ||||||| | || || || ||||| ||||||||||||||||||||| || || ||||| |||||||| ||||||||||||| || ||||||||||| ||||| ||
gtatgttgatattgcatttgtttttttggagtaaatttaccctatgaaacatacatttgagtgttcttatggatatggttctatgtcatctttcttatagTACCATCTCACTTGGAGAAAGTTTTGAGAGAACAAATTGCTGAGGGACAACCCCGGACACATAGACCATGGAAGAAGATAATTGTTGTTGTGGAAGGAAT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 6
---gtaagcatttgttgtgtttc---agcttcagaggttctttcca-tataatgga--tggcttacatgtatattctcttgcttgtgtttct-----tagCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
||| | || | |||| | || | ||||| | | |||| || | || |||| | | |||| ||| || | ||| || || |||||||| ||||||||||||||||||||| ||||| || || ||||| ||| |||| |||||||| || || |||||||| || || ||
gcattaattttctgcttggttttcctgaatgcacatactctttggaatttaattgaaatattttccatgctttgtttctttattgccattttgcttccagCACCCTCTCATTTGGAGGAAGTTTTGAGAGAACAAATTGCTGAAGGACAGCCCAGGACGCATAGACCTTGGAAGAAGATCATAGTTGTTGTGGAGGGAAT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S377_35V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtaagcatttgttgtgtttcagcttcagaggttctttccatataatggatggcttacatgtatattctcttgcttgtgtttctt-----agCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
| || | ||| || | || | |||| ||| | || |||| | || | |||| | ||| || || ||||| || | ||| | ||||| |||| | |||| || | | |||||| | |||||||||||||||||||| ||| ||||||||||
gcgttttgttctcgttttcgatgtattaacacctccccgtagctttgtgtattactgacactgggactgtagaactaaatgtgcttttttccttgaacagCTCCATCACATTTAGAGCAAGTGCTTCGAGAAGCAATTTCCCAAGGACAGGCCCGAACACATAGGCCATGGAAGAAAATTATTGTCGTTATTGAAGGTATMapped 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|86059362|gb|DR355119.1|DR355119EST: TGGTGCTCGAGGTTCTGGAGCCACTATCCGTGTTTTCCAGCATAACA CGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAAC
genomic: TGGTGCTCGAGGTTCTGGAGCCACTATCCGTGTTTTCCAGCATAACAgtaagcattt ... tgtttcttagCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttccatataatggatggcttacatgtatattctcttgcttgtgtttcttagCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
ggcttac putative branch site (score: 3)
tgtttctt putative PPT
atgtatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatttgttgtgtttcagcttcagaggttctttccatataatggatggcttacatgtatattctcttgcttgtgtttcttagCGCCTTCCCATTTGGAACGAGTTTTGAGAGAACAAATTGCAGAAGGTCAACCTAGGACACATCGACCATGGAAGAAAATTATTGTTGTTGTTGAAGGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG