Sequence
atgc intronic sequence ATGC exonic sequence...tacctctggtttgatgtggatgcttctcatcctaaatgagtttctggatttagggccctatactgtgctatgaaaaattgacctggatctccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G315931_T02 (Zea mays), 3'ss of exon 15
---------------------------------------------------------------tacctctggtttgatgtggatgcttctcatcctaaatgagtttctggatttagggccctatactgtgctatgaaaaattgacctggatctccttg-tgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT
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gtaatttctttcactgcagtttggaatttttttgtatcaatcaagtgtaaaacattgcggtcatttctttacatacctgacgttgctgtataactcaatagattccctttccccctagtcccctacca--ctatgattcttaaaaatatgtcccttcgatgcagCTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT
upper sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G07710.1 (Glycine max), 3'ss of exon 15
-tacctctggtttg-atgtggatgcttctcatcctaaatgagtttctggatttagggccctatactgtgctatgaaaaattgacctggatctccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT
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atatggacactatatgtgcacccacaatactttttggatgtttatttagataatggaatgtatatattatta--gacgactaatctgtttatttaattgcagATAGTTGATGCCTTGGAGCTTAGCAGACTGACCATGAATACTATAAAACAAAATCTTTGGTGGGCTTTCATATACAACATT
upper sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 15
-tacctctggtttgatgtggatgcttctcatcctaaatgagtttct---ggatttagggccctatac-tgtgctatgaaaaattgacctggatctccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT
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gaaactgcattttcttactaa-atcaatgataatagatgtttccctttggctttcatgaatttggacacatgaacttagtagtta--catgatttcc--atgcagTTGCTTGATGCGATGGAGCTAAGTCGGCAAACCATGAAGACCGTGAAGCAAAACCTTTGGTGGGCGTTCGGATACAACATT
upper sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G33520.3 (Arabidopsis thaliana), 3'ss of exon 15
-tacctctggtttgatgtggatgcttctcatcctaaatgagtttct---ggatttagggccctatac-tgtgctatgaaaaattgacctggatctccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT----
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gaaactgcattttcttactaa-atcaatgataatagatgtttccctttggctttcatgaatttggacacatgaacttagtagtta--catgatttcc--atgcagTTGCTTGATGCGATGGAGCTAAGTCGGCAAACCATGAAGACCGTGAAGCAAAACCTTTGGTGGGCGTTCGGATACAACATTGTAAMapped 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|110427460|gb|EC993897.1|EC993897EST: CTGCTAGTGAGGTGTCTTCTATTGTCCTGATGGGCAACAGGCTTTCACAG TTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAA
genomic: CTGCTAGTGAGGTGTCTTCTATTGTCCTGATGGGCAACAGGCTTTCACAGgtattttctg ... ccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAA
EST:
gi|110371518|gb|EC935604.1|EC935604EST: CTGCTAGTGAGGTGTCTTCTATTGTCCTGATGGGCAACAGGCTTTCACAG TTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAA
genomic: CTGCTAGTGAGGTGTCTTCTATTGTCCTGATGGGCAACAGGCTTTCACAGgtattttctg ... ccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatttagggccctatactgtgctatgaaaaattgacctggatctccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT
aattgac putative branch site (score: 3)
tctccttgt putative PPT
tatgaaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacctctggtttgatgtggatgcttctcatcctaaatgagtttctggatttagggccctatactgtgctatgaaaaattgacctggatctccttgtgcagTTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - tggtttg
- - - - - - - - -ggatgct
- - - - - - - - - - - - -ctcatcc
- - - - - - - - - - - - - - - - -aaatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgga