Sequence
atgc intronic sequence ATGC exonic sequence...gatatctttgagtgaactggaactttatggataacataaaattattctaattgaattatctatcctcgtgatgacaacaatgttgaataattctgtgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCTCCAATAGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 4
------------------------------------------------gatatctttgagtgaactggaactttatggataacataaa---attattctaattgaattatctatcctcgtgatgacaacaa---tgttgaa----taattctgtgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCTCCAATAGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCT
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gtatcagatcatatttggcagtcacttcattaggcctattttttcagtggtgacttgctgtggtcacttgccttgtactttgcatttacttattattgtgttggctccacgaatgttagttttggcaaaaaatttagtgaagtggtcattctgtgcagGTGTTTGGTCCAGCATCGAAGCAGAAGGATTTGTTTGAGCAATCTATCTCACCAATAGTAAATGAGGTCCTTGAGGGCTATAATTGCACAATTTTTGCTT
upper sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G40580.1 (Glycine max), 3'ss of exon 3
--gatatctttgagtgaactggaactttatggataacataaaattattctaattgaattatctatcctcgtgatgacaacaatgttgaa--taattctgtgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCTCCAATAGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCT
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tacctactctcttatcaatcctaatcatgatattgataaggaa--ggcctcacacgttttttta--cttgttattggaataaaattgtccttgttttggcgtagGTGTTTGGTCCTAACTCTCAACAGAAAGAACTGTATGATCAGGCAGTGTCTCCAATTGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGT
upper sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 2
gatatctttgagt--gaactggaactttatggataacataaaattattctaattgaattatctatcctcgtgatgacaacaatgttgaataattctg-tgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCTCCAATAGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCT
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gatattgataaggaagaccttacacgtttttcttttatccttgttatcggaataaaattatc---ctgtgtgattatgctgattttggtttgttttggcgtagGTGTTTGGTCCTAACTCTCAACAGAAAGAACTGTATGATCAGGCAGTGTCTCCCATTGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGT
upper sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 2
gatatctttgagtgaactggaactttatggataacataaaattattctaattgaattatctatcctcgtgatgacaacaatgttgaataattctgtgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCTCCAATAGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCT
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gttttggtttagtct-ttaaggctttttagataatgtgca-tcattataggtttctgacagaaagt-atcatgcttataa-gttggtgaaatttg-atagGTTTTTGGCCCAACATCCCAGCAAAAGGATCTGTATCATCAAGCAGTTTCTCCAATTGTCTTTGAGGTTCTTGATGGGTATAACTGCACCATCTTTGCATMapped 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|30301488|gb|CB978282.1|CB978282EST: TGCAGAATATTGCTAACAAGCAGATTGATAGAACTTTTATGTTCGATAAG GTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCT
genomic: TGCAGAATATTGCTAACAAGCAGATTGATAGAACTTTTATGTTCGATAAGgttttgtttg ... ttctgtgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaattgaattatctatcctcgtgatgacaacaatgttgaataattctgtgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCTCCAATAGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCT
ttctaat putative branch site (score: 2)
aatgttgaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatatctttgagtgaactggaactttatggataacataaaattattctaattgaattatctatcctcgtgatgacaacaatgttgaataattctgtgtagGTCTTTGGTCCAACATCCCAACAAAAGGACTTGTATGATCAAGCTGTGTCTCCAATAGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCT
- - - - - - - - - - - - - - ggataac
- - - - - - - - - - - - - - - - - - -aaaatta
- - - - - - - - - - - - - - - - - - - - - - - - aattgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaacaa