Sequence
atgc intronic sequence ATGC exonic sequencegtaacaatattctctttatcttttccttgtttcataacctatgaagaagagtggaaaaaatgcagtttctttcatttgattcatggactggtttgttgcagGACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCATTGAGCGTTGCAACAGAGATGGTAGCGGAACTGGATATGGACGATCATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04910.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 6
----gtaacaatattctctttatcttttccttgtttcataacctatgaagaagagtggaaaaaatgcagtttctttcatttgattcatggactggtttgttgcagGACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCATTGAGCGTTGCAACAGAGATGGTAGCGGAACTGGATATGGACGATCATGG
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gtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaa---aaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv14s0030g01660.t01 (Vitis vinifera), 3'ss of exon 6
gtaacaatattctctttatcttttccttgtttcataacctatgaagaagagtggaaaaaatgcagtttctttcatttgattcatgga-ctggtttgttgcagGACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCATTGAGCGTTGCAACAGAGATGGTAGCGGAACTGGATATGGACGATCATGG
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gtcaaaagatcatct---ccttttgcctttttttttttttttgttattgtttg------attttccttcct-caaatgaagcatggaactctctctttgcagACCACATTCGTAACATCTATTTCCCATTCGACATTGAGATGGATACAGCATTGAGCGTTGCAACTGAAATGGTTGCTGAACTGGATATTACAGACCAAGAMapped 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|47830850|gb|CK120534.1|CK120534EST: GAGAGATGATGGTGGCTTGTTCTTGCGTCTTAGGATCGCTGACAAAGAAG GACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCAT
genomic: GAGAGATGATGGTGGCTTGTTCTTGCGTCTTAGGATCGCTGACAAAGAAGgtaacaatat ... tttgttgcagGACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagtggaaaaaatgcagtttctttcatttgattcatggactggtttgttgcagGACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCATTGAGCGTTGCAACAGAGATGGTAGCGGAACTGGATATGGACGATCATGG
atttgat putative branch site (score: 5)
aaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaatattctctttatcttttccttgtttcataacctatgaagaagagtggaaaaaatgcagtttctttcatttgattcatggactggtttgttgcagGACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCATTGAGCGTTGCAACAGAGATGGTAGCGGAACTGGATATGGACGATCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG