Sequence
atgc intronic sequence ATGC exonic sequence...ttcttgaattgtcttatgtatgtgaattgtggcagatctatttgtttgtttgttttcgattttgctaatggagtgttgttgtttcttttctgttataaagGGTCCAGAAATCCGAACCGGGTTCTTGAAAGATGGGAAACCAATCCAGCTGAAACAAGGACAAGAGATCACTATTTCGACTGACTATGACTTGAAGGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56350.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g00130.t01 (Vitis vinifera), 3'ss of exon 1
ttcttgaattgtcttatgtatgtgaattgtggcagatcta---tttgtttgtttgttttcgattttgctaatggagtgttgttgtttcttttctgttataaagGGTCCAGAAATCCGAACCGGGTTCTTGAAAGATGGGAAACCAATCCAGCTGAAACAAGGACAAGAGATCACTATTTCGACTGACTATGACTTGAAGGGTG
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atgacgagcttctttgtggttatggtat-catcaaattgagaactaaaaaattaaagtggaattttcccaattgtttat--ttcatctgcaaatgtcaaacagGGTCCAGAAATTCGAACCGGGTTTTTGAAGGATGAAAAGCCCATCCATCTGAAGCAAGGCCAAGAGATCACCATATCCACTGACTATAACATAAAGGGTGMapped 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|164208792|gb|ES014299.1|ES014299EST: CTATGCTTAACACTGGGATTCTCTGTGCCGTCATGCTCGACACCAAG GGTCCAGAAATCCGAACCGGGTTCTTGAAAGATGGGAAACCAATCCAGCTG
genomic: CTATGCTTAACACTGGGATTCTCTGTGCCGTCATGCTCGACACCAAGgttcgattac ... tgttataaagGGTCCAGAAATCCGAACCGGGTTCTTGAAAGATGGGAAACCAATCCAGCTG
EST:
gi|164172736|gb|ES109589.1|ES109589EST: AAGCTATGCTTAACACTGGGATTCTCTGTGCCGTCATGCTCGACACCAAG GGTCCAGAAATCCGAACC
genomic: AAGCTATGCTTAACACTGGGATTCTCTGTGCCGTCATGCTCGACACCAAGgttcgattac ... tgttataaagGGTCCAGAAATCCGAACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttgttttcgattttgctaatggagtgttgttgtttcttttctgttataaagGGTCCAGAAATCCGAACCGGGTTCTTGAAAGATGGGAAACCAATCCAGCTGAAACAAGGACAAGAGATCACTATTTCGACTGACTATGACTTGAAGGGTG
tgctaat putative branch site (score: 2)
ttgttgtttcttttct putative PPT
ttttctgttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttgaattgtcttatgtatgtgaattgtggcagatctatttgtttgtttgttttcgattttgctaatggagtgttgttgtttcttttctgttataaagGGTCCAGAAATCCGAACCGGGTTCTTGAAAGATGGGAAACCAATCCAGCTGAAACAAGGACAAGAGATCACTATTTCGACTGACTATGACTTGAAGGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattttg