Sequence
atgc intronic sequence ATGC exonic sequencegttttgtatctttttctcgtgaaactagcttttctgcatcctgtttaattctgcattttgaacgctttgtttctcttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGAATGGAGATTATGAATTTGCTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57410.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57410.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------gttttgtatctttttctcgt-gaaactagcttt--tctgcatcctgtttaattctgcatt--ttgaacgct-----ttgtttctcttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGAATGGAGATTATGAATTTGCTACAG
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gtgtgacatctttgattttttattttttttattctgatgagaaccatatttggtgattagtgctcttacatgataggaacttacacaagtccacctattattagatttggaaatgaataagggctggtattttttgtatttgcagGAGAGGCTAAACCAAGTGTTGATGGAGAAGAAGAAAGAGTCTAGGTCAGGCATGGAGATAATGAATTTGCTTCAG
upper sequence: AT5G57410.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 7
-------------------------------------------------gttttgtatctttttctcgt--gaaacta-gcttttctgcatcctgtttaattctgcattt-tgaacgctttgtttctc----ttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGAATGGAGATTATGAATTTGCTACAG
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gtgtgatatctttgattttgtttttattctgatgagaaccatatttggtgattagtgcttttacatgataggaacttacgcgggtccacatattattagatttggaaatgatgaagggctggtattttgtatttgcagGAGAGGCTAAACCAAGTGTTGATGGAGAAGAAGAAAGAGTCTAGGTCAGGCATGGAGATAATGAATTTGCTTCAG
upper sequence: AT5G57410.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------------------------------------gttttgtatctttttctcgtgaaactagcttttctgcatcctgtttaattctgcattttg----------aacgctt-tgtttctcttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGAATGGAGATTATGAATTTGCTACAG
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gtaggatcctttccatgtgtattattatgatattatcttttaggggaaacttaaaggttgctcatgttagcaaatgggaacatctttcatgaatgacaacatatatggagaacaggagaagttcatgagtaggaaattggggaatgattgtgtttcacttgcagGAGAGGCTTAACCAAGTTTTGATGGAGAAAAAGAAGGAATCGAGGTCTGGCATGGAGATAATGAATCTTCTTCAGMapped 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|86047423|gb|DR343178.1|DR343178EST: AACAGATACACGAAATGAAGAAAAAGGAGAAGGATTACATTAAGTTGCAG GAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGA
genomic: AACAGATACACGAAATGAAGAAAAAGGAGAAGGATTACATTAAGTTGCAGgttttgtatc ... tctcttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGA
EST:
gi|86047424|gb|DR343179.1|DR343179EST: AACAGATACACGAAATGAAGAAAAAGGAGAAGGATTACATTAAGTTGCAG GAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGA
genomic: AACAGATACACGAAATGAAGAAAAAGGAGAAGGATTACATTAAGTTGCAGgttttgtatc ... tctcttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttttctgcatcctgtttaattctgcattttgaacgctttgtttctcttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGAATGGAGATTATGAATTTGCTACAG
gtttaat putative branch site (score: 4)
cgctttgtttctctt putative PPT
tgtttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgtatctttttctcgtgaaactagcttttctgcatcctgtttaattctgcattttgaacgctttgtttctcttgtagGAACGGCTGAATCAAGTGTTAATGGAGAAAAAGAAAGAATCAAGATCTGGAATGGAGATTATGAATTTGCTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT