Sequence
atgc intronic sequence ATGC exonic sequencegtttgcttcctcttcttttaccccttagtaaatggtaaattagtctcattttgaatatcaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42020.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 7
gtttgcttcctcttcttttaccccttagtaaatggtaaattagt-ctcattttgaatatcaaaataattatcctgatctcgttt--tga------cagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
| | |||| | | ||||||| | ||| |||||| | | ||| | | | | || | ||| ||| || || || || |||||||| || || || ||||||||||||||||| || || ||||| || |||||||||| | || || || |||||||| ||
---------gtgagcagctaccggagtccgga-gataaattattactctttttgatgaatggacgaatgaatccagtgttgtctgatgaactgtgcagGGGCACACCCCAGATCGAGGTGACCTTCGAGGTGGACGCCAACGGTATCCTAAACGTGAAGGCGGAGGACAAGGGCACGGGCAAGTCGGAGAAGATCACG
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 7
gtttgcttcctcttcttttaccccttagtaaatggtaaatt-agtctcattttgaatatcaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
|| | | | || || | | || | ||||| ||| | || | ||| | || |||| ||| ||| || || || || |||||||| || || || ||||||||||||||||| || || ||||| || |||||||||| | || || || |||||||| ||
gtgcgttgctgctgctcat-ctttttgttgaatggccgattgaatccagtgttgtctgatgaacgaattgaactgt----------gcagGGGCACACCCCAGATCGAGGTGACCTTCGAGGTGGACGCCAACGGTATCCTGAACGTGAAGGCGGAGGACAAGGGCACGGGCAAGTCGGAGAAGATCACG
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 7
-------------gtt--tgcttcctcttcttttaccccttagtaaatggtaaattagtctcattttgaatatcaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
||| || | | || | | | | ||| | || |||| | | | | || ||||| | | || |||| || ||||||||||| || || || || ||||| || |||||||| ||||| |||||||| ||||| ||||||| | |||||||||||| ||||| ||
gtttgttacctgcgttgatgatgcagtgtcctct-ctcattattgctccatatattaatgttagtaaattcattggtggtattatatttgggtaattg-aacagGGGCACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGAACTGGTAAATCAGAAAAGATCACC
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 7
gtttgcttcctcttcttttaccccttagtaaatggtaaattagtctcattttga-atatcaaaataattatc--ctgatctcgt--tttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
|||| | ||| | | | | || | ||| |||| ||| | | | || | ||| | || | || || |||| || ||||||||||| || || || || ||||| || |||||||| ||||| |||||||| ||||| ||||||| | |||||||||||| ||||| ||
gtttattacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
gtttgcttcctcttcttttaccccttagtaaatggtaaattagtctcattttga-atatcaaaataattatc--ctgatctcgt--tttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
||||| | ||| | | | | || | ||| |||| ||| | | | || | ||| | || | || || |||| || || |||||||| || || || || ||||| || |||||||| ||||| |||||||| ||||| ||||||| | |||||||||||| ||||| ||
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 7
gtttgc----ttcctcttcttttaccccttagtaaatggtaaattagtctcattttgaatatcaaaataattatcctgatctcgttttga-cagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
|||||| || || || | | ||||| || | ||| || | | || ||| || | |||| ||| |||||||| ||||| || ||||| |||||||| ||||| || ||||| || ||||| || || |||||||||| | ||||||||||||||||| ||
gtttgcgaaacctgtccactccaactcttctgtaaa--atactcctactgtaggcagaa-attgatgtgataatctgattcctatgttgaacagGGGAACCCCACAAATTGAAGTCACGTTTGAAGTTGACGCAAATGGTATCCTAAATGTCAAGGCTGAGGACAAGGGCACGGGTAAATCAGAGAAGATCACCMapped 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|125065013|gb|EL132409.1|EL132409EST: TGCAGGCTACTCGGGAAATTCGACCTCACTGGAGTCCCACCGGCCCCAAG AGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCT
genomic: TGCAGGCTACTCGGGAAATTCGACCTCACTGGAGTCCCACCGGCCCCAAGgtttgcttcc ... gttttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCT
EST:
gi|125259684|gb|EL273769.1|EL273769EST: TGCAGGCTACTCGGGAAATTCGACCTCACTGGAGTCCCACCGGCCCCAAG AAGGAAACCCCTCAAATCGAGGTCACATTTGAAGTG
genomic: TGCAGGCTACTCGGGAAATTCGACCTCACTGGAGTCCCACCGGCCCCAAGgtttgcttcc ... gttttgacagA-GGAA-CCCCTCAAATCGAGGTCACATTTGAAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaattagtctcattttgaatatcaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
tcctgat putative branch site (score: 3)
tctcgtttt CT-rich tract
tctcattttgaatatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcttcctcttcttttaccccttagtaaatggtaaattagtctcattttgaatatcaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA