Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcaagattctctttaaacattttaacaagagaggatatttctgatgcttttcatcaacagtcttttcttgttctcatttgcttgtagCTTGATACATCAGCGTTCATGGATGAGTTTGGTTTACCTTCAAAGACGAGAACAAAGGACGGATATAACCCCTTACTTGATGACTTCAAGAACACTAAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04900.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G03240.1 (Glycine max), 3'ss of exon 8
gtaaatcaagattctctttaaacattttaacaagagaggatatttctgatgcttttcatcaacagtcttttcttgttctcatttgcttgtagCTTGATACATCAGCGTTCATGGATGAGTTTGGTTTACCTTCAAAGACGAGAACAAAGGACGGATATAACCCCTTACTTGATGACTTCAAGAACACTAAGT------------------------
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--------------------------------------------------------------------------gtttatatttgat-gtagctagaaacatcatctttcatggagGAGTTTGGTTTGCCCACAAAAACAAGAACCAAGGACGGATACAACCCACTCTTGGATGACTTCAAGAATACCAAATTTTATCTTAGCGTCCCTACACACA
upper sequence: AT1G04900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0136g00320.t01 (Vitis vinifera), 3'ss of exon 2
------gtaaatcaagattctctttaaacattttaacaagagaggatatttctgatgcttttcatcaacagtcttttcttgttctcat---ttgcttgtagCTTGATACATCAGCGTTCATGGATGAGTTTGGTTTACCTTCAAAGACGAGAACAAAGGACGGATATAACCCCTTACTTGATGACTTCAAGAACACTAAGT
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ttttctatagatttgagtctcgtctatacatatttttagtttcacaattttattctaactttctttg-cattcttgtcaaatatatataaattggatgtagCTTGATACGTCCTCATTCATGGAGGAATTTGGCCTGCCCTCAAAAACGAGAACCAAAGATGGATACAACCCACTGCTGGATGACTTCAAGAACACTAAATMapped 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|125040765|gb|EL113034.1|EL113034EST: AGGCGAACTCTCACT CTTGATACATCAGCGTTCATGGATGAGTTTGGTTTACCTTCAAAGACGAGA
genomic: AGGCGAACTCTCACTgtaaatcaag ... ttgcttgtagCTTGATACATCAGCGTTCATGGATGAGTTTGGTTTACCTTCAAAGACGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatatttctgatgcttttcatcaacagtcttttcttgttctcatttgcttgtagCTTGATACATCAGCGTTCATGGATGAGTTTGGTTTACCTTCAAAGACGAGAACAAAGGACGGATATAACCCCTTACTTGATGACTTCAAGAACACTAAGT
ttctgat putative branch site (score: 3)
tcttttcttgttctca putative PPT
ttttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcaagattctctttaaacattttaacaagagaggatatttctgatgcttttcatcaacagtcttttcttgttctcatttgcttgtagCTTGATACATCAGCGTTCATGGATGAGTTTGGTTTACCTTCAAAGACGAGAACAAAGGACGGATATAACCCCTTACTTGATGACTTCAAGAACACTAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC