Sequence
atgc intronic sequence ATGC exonic sequence...atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G42810.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 7
-atcttgaatttattggctaaccttctactcc-ctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttg-acacattgtttg-cttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
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cttcttttatcctgttgc-atcattttgcttggcttttgaattttttt---ctttaatttttaaccttgcaatttcattagtatttgttttccatcttctgcagTACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCTTTTTCAT
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 7
----atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtt-tgacacattgtttg-cttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG-
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gaaggtcctccatc-attgcagggcatttgtat---ttttgtatttttat---ctttaatttttaactttgcaaattcattattatttgttttctgtcttctgcagtACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCCTTTTCATT
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 1
atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG------------------------------------------------
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------------------------------------------------------------------------------------tgatatgctt--gcagttctatgatctattaaatatttttgacctcaatggacttccctcagaagagaacccctatctatttaatggtgattttgtggatagAGGATCCTTTTCTTTAGAGGTCATCCTCACACTGTTTGCATTTAAGTGCATGTCTCCATCAG
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S87_139V6.2 (Physcomitrella patens), 3'ss of exon 7
--------atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttt--tgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
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gtactataaaattctttgtaggggcaatgctttgtattttccgtgtgttacttcatgacttggtgtttgacat--gatttctaactaggaggatgatggaattgacgcagTACTATGACTTGCTGAACATTTTCAAGCTTAATGGTCTCCCCTCGGAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCATTTTCGGMapped 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|124982622|gb|EL055414.1|EL055414EST: GTGTTCCACATGGCAAACATATCACTGTTTGCGGTGACGTTCATGGTCAG TTCTACGATCTTCTCAATA
genomic: GTGTTCCACATGGCAAACATATCACTGTTTGCGGTGACGTTCATGGTCAGgtatgctttg ... gcttttgcagTTCTACGATCTTCTCAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
gtttgac putative branch site (score: 4)
tttgctttt putative PPT
ttgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
- - - - - - - -gctaacc
- - - - - - - - - - - - - -ctccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttga