Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGGAAGTAGTATTTGATAAGATTCGTTACTCAAGAGATACAAAACTTAGCATTGGACTTGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G09810.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G08700.1 (Glycine max), 3'ss of exon 3
gtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGGAAGTAGTATTTGATAAGATTCGTTACTCAAGAGATACAAAACTTAGCATTGGACTTGTTC
|| | | | || ||| | | || || || || | | | | || ||| || ||||||||| ||| | || ||||| |||||||||||| | |||||||| || | || |||||||| || |||||||| |||||||| ||||| || ||||||
gtgagttgggctgagctttatctattggttaattcattaatgccttcagaagttatattcactttttagccattgacagATTGCGAAGTTAAGTATGATCCCTGTATCATGCCTATTGGAAGTTGTTCTCGACAAGATTCGGTATTCAAGAGACACAAAACTGAGCATAGGTGTTGTTC
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G36620.1 (Glycine max), 3'ss of exon 2
gtaaat-gtgtttgctttttg-tgtta-tgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGGAAGTAGTATTTGATAAGATTCGTTACTCAAGAGATACAAAACTTAGCATTGGACTTGTTC
|| | | || || |||| | || | || || || || | | | |||| || | || |||||||| ||| | || ||||| |||||||| ||| |||||||||| | || || || ||||| || ||||||||||||||||| ||||| || |||| |
gtgagttgtattgaattttcactattggtccaaggtccattaatgcattcagaagttaaattttcttcttaaccattggcagATTGCTAAGTTGAGTATGATCCCTGTATCCTGCCTGTTGGAAGTTTTTTTCGACAACATTCGGTATTCAAGAGATACAAAACTGAGCATAGGTGTTGTAC
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G27820.1 (Glycine max), 3'ss of exon 2
gtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaat-ggtgtcttctcttttatgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGGAAGTAGTATTTGATAAGATTCGTTACTCAAGAGATACAAAACTTAGCATTGGACTTGTTC
|| | | | || ||| | | || | || | || | | | | || ||| || ||||||||| || | || ||||| |||||||||||| | |||||||| || | || |||||||| || |||||||| |||||||| ||||| | ||||||
gtgagttgggctgagctttatctattggttcattcactaatgccttcagaagttaatattcactttttagccattgacagATTGCGAAATTAAGTATGATCCCTGTATCATGCCTATTGGAAGTTGTTCTCGACAAGATTCGGTATTCAAGAGACACAAAACTGAGCATATGTGTTGTTCMapped 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|125104185|gb|EL158345.1|EL158345EST: TTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAG ATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGG
genomic: TTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgt ... tgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGGAAGTAGTATTTGATAAGATTCGTTACTCAAGAGATACAAAACTTAGCATTGGACTTGTTC
ttctaat putative branch site (score: 2)
tcttctcttttatgct putative PPT
tcttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGGAAGTAGTATTTGATAAGATTCGTTACTCAAGAGATACAAAACTTAGCATTGGACTTGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA