Sequence
atgc intronic sequence ATGC exonic sequence...gaactgcttgcttgatattctaggacttctaacaaatgtttgtttgtggatccattttggtttaatccttttaatacatgttcatttcttgcaagggcagATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCAGAAGAGAACCAGAAGACACTAGAGGTTTTAAAAGAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 5
gaactgcttgcttgatattctaggacttctaacaaatgtttgtttgt-ggatccattttggtttaatccttttaatacatgttcattt---cttgcaagggc-agATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCAGAAGAGAACCAGAAGACACTAGAGGTTTTAAAAGAGAG
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--agaattctctagat-ccccaacatctttaaaattcaattataaattagacctaactgtctttcatgatttt--tactttgtcatttgaatctatgtgaattagATGGAAGAGAAAGTGAAAGAAATTGTGGAGATTAAGCAACGCAGTCTGGCAGAAGAGAATCAGAAAACAATGGAAGTTTTGAAAGAAAG
upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G09890.2 (Glycine max), 3'ss of exon 4
-gaactgcttg----cttgatattctaggacttctaacaaatgtttg-tttgtggatccattttggtttaatccttttaatacatgttcatttcttgcaagggcagATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCAGAAGAGAACCAGAAGACACTAGAGGTTTTAAAAGAGAG
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agaattctctagatccccgacatctttaaaattcaattacaaattagacctaactgtctttcatgatttttactttgtcatttgaatttatgt------gaattagATGGAAGAGAAAGTGAAAGAAATTGTGGAGATTAAGCAACGCAGTCTGGCAGAAGAGAATCAGAAAACATTGGAAGTTTTGAAAGAAAG
upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S168_102V6.1 (Physcomitrella patens), 3'ss of exon 4
---gaactgcttgcttgatattctaggacttctaacaaatgtttgtttgtggatccattttggtttaatccttttaatacatgttcatttcttgcaa-gggcagATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCAGAAGAGAACCAGAAGACACTAGAGGTTTTAAAAGAGAG
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ttctcacagtctacct--tattctagg-tgcataatcgttgtc-gcttttgggttaaccttatttacgctgatgaggtcaatggttgtcaaatatgatgaacagATGGAGGAGAAAATTAAGGAAATCGTGGAGATGAAACAGCGCAGCTTGGCAGAGGAGAATCAGAAAAGCTTGGAAATATTACGAGACAG
upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ26077 (Selaginella moellendorffii), 3'ss of exon 4
gaactgcttgcttgatattctaggacttctaacaaatgtttgtttgtggatccattttggtttaatccttttaatacatgttcatttcttgcaagggcagATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCAGAAGAGAACCAGAAGACACTAGAGGTTTTAAAAGAGAG
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---------------------------------------------gtgagtcactaacgtttataacggcttcttat-tatcttgtggaatcattttcagATGGAAGAAAAGGTAAAGGAGCTTGTGGAAATGAAACAGCGCAATCTGGCCGAGGAGAACCAGAAGATTCTTGAAGTTCTCAAGGAAAGMapped 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|30301790|gb|CB978584.1|CB978584EST: AGGCAACAATAAGAAGACTTGAAGAGCGTAATCGCCAGTTAGAACAACAG ATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCA
genomic: AGGCAACAATAAGAAGACTTGAAGAGCGTAATCGCCAGTTAGAACAACAGgttggtactg ... gcaagggcagATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggatccattttggtttaatccttttaatacatgttcatttcttgcaagggcagATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCAGAAGAGAACCAGAAGACACTAGAGGTTTTAAAAGAGAG
ttttaat putative branch site (score: 3)
tttcttgc putative PPT
tttaatccttttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaactgcttgcttgatattctaggacttctaacaaatgtttgtttgtggatccattttggtttaatccttttaatacatgttcatttcttgcaagggcagATGGAGGAGAAGGTGAAGGAAATTGTGGAAATGAAGCAACGCAGTTTGGCAGAAGAGAACCAGAAGACACTAGAGGTTTTAAAAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - -gcttgct
- - - - - - - - - - - - - - - aacaaat
- - - - - - - - - - - - - - - - - - - - - - - -ggatcca