Sequence
atgc intronic sequence ATGC exonic sequencegtaatggttcagtctttacacaatatatctaactatgatggtttcagttgttaatattgtcatgttcgttcatagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48960.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 8
gtaatggtt-cagtctttacacaatatatctaac-tatgatg-gtttcagttgttaatattgtcatgttcgttca-tagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
||| || || ||| | | | | | || | || ||| | ||| | | | | | || | ||| | | |||| || || || || | ||||| || ||||| |||||||| || ||| ||||||||||| | |||||||| || | |||||||||||||||||||| |
gtattgcttatagtatgtgtatc-tctgcctcgcacataatgtgcttctgctcattacttggttgttttcatgaaacagGCAGGCAAAAAACTTGTACTTATTACCAACTCAGATTATCATTATACACACAAAATGATGCATCATTCATTCAATAGATTCCTTCCCAATGACATGGGTT
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 9
---------gtaatggttcagtctttacacaatatatctaactatgatggt-ttcagttgttaatattgtcatgttcgttca-tagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
||||| || | ||| || || |||| ||| ||| ||| || | || | || | ||| | | ||||||| ||||| || |||| || || ||||| ||||||| |||||||||||||||||| ||||||| ||||| | |||||||||||| || |||| |
gtattacttctaatgttttatattttgcataacatat-----tataatgcccttctactgcttatttagttgtcttcatgaaacagGCTGGCAAGAAACTTCTGCTAATTACCAACTCAGATTATCTTTACACAGACAAAATGATGCAGCATTCTTTTAATAGATTCCTTCCCAACGATATGGGTT
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 9
gtaatggttcagtctttacacaatatatctaac-tatgatggt-ttcagttgttaatattgtcatgttcgttca-tagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
||| | ||| | | | | | |||| ||| || ||| || | || | || | ||| || | ||||||| || || || | || || || ||||| ||||||| |||||||||||||||||| |||||| ||||| | |||||||||||| || |||| |
gtattacttctaatgctttatattttgcataacatataattcccttctatttcttatttagttgtcttcattaaacagGCTGGCAAAAAACTTCTACTAATTACCAACTCAGATTATCTTTACACAGACAAAATGATGCGGCATTCTTTTAATAGATTCCTTCCCAACGATATGGGTT
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 9
--------gtaatggttc-agtctttacacaatatatctaactatgatg-gtttcagttgttaatattgtcatgttcgttcat-agGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
||| ||| ||||||| | | | || | | | | | || || | | | || | | || ||||||| || ||||| |||||||| || ||||| |||||||| || ||||||||||||||| ||||||| ||||||||||||||||| ||||| |||| ||
gtatgcttataactcttctagtctttgt--gacaggtgaaattgttgtaagatctccttattcacttggatattcttttctatcagGCTGGCAAAAAGCTTTTGCTTATTACCAACTCAGATTATCATTATACAGACAAAATGATGCAGCATTCCTTTAACAAATTCCTTCCAAATGATATGGGCT
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S55_42V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------------------gtaatggttcagtctttacacaatatatctaactatgatggtttcagttgttaatattgtcatgt-tcgttcatagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
| || | | || | | || | | | | | | | || | | ||| | ||| || || |||||||||||||||| ||||||||||| || || ||||||| |||||| |||| |||||| | | | ||| | |||| || || |||| ||| | |
gtttgaatatcaacctgcttgcagtgtatttttcgtcacaatcgagtggatttacaattactgaatatgagaagtcgaaccattgtagagtaattttcaattcgtcaggtgcaatcgataagtaatttgtgtctctttttcagGCTGGTAAGAAGCTATTGCTTATCACGAATTCTGATTATCTCTACACGAACAAGATGATGCAATACGCTTTTGATAAATATCTCCCAAATGGTATGAATTMapped 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|125065477|gb|EL132692.1|EL132692EST: TCTTTTAGATCAAAAGGAG GCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGAC
genomic: TCTTTTAGATCAAAAGGAGgtaatggttc ... tcgttcatagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatatctaactatgatggtttcagttgttaatattgtcatgttcgttcatagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
ttcgttc CT-rich tract
ttgttaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggttcagtctttacacaatatatctaactatgatggtttcagttgttaatattgtcatgttcgttcatagGCTGGTAAGAAGCTCTTGCTTATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA