Sequence
atgc intronic sequence ATGC exonic sequence...gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g36790.1 (Oryza sativa), 3'ss of exon 1
-------gaattg----tttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
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gatgtggtaattgacattattttattattatcttatggtgattttacctttaatt----gaacttccaagatg-atgagtggccacaatttcttt------ccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG
upper sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G01820.1 (Glycine max), 3'ss of exon 1
gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
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-----------------------gtacatacatctccttctttattaactactcattcatttt-----tgtctt---ttttattattctgctctgt--agATTCAATTGGTTAGAATTCAAGTTAGAGTACCTGAGTATGGTTGGACTACTCAGAAGATTTTTCATCTCATGAACTTCATTGTCAACGGAG
upper sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G38920.2 (Glycine max), 3'ss of exon 1
gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
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---------------------gtacatacatct---cctccttctttaacta-ctcactcttttttgtctttt----ttactctattctgcactgt--agattcaattggtcagAATTGAAGTTAGAGTACCTGAGTATGGCTGGACTACGCAGAAAATTTTTCATCTCATGAACTTCATTGTCAACGGAG
upper sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G21790.1 (Arabidopsis thaliana), 3'ss of exon 1
----------gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
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ttgtatagtttgattgattgtttctgtagtttatttctgggtttag-ttagttgtgttgcaatttc----tgaccttttgtttgaaatgggatt-atg---attg-gtagGTTCAACTGATAAGGATCCAAATGAGAGTGCCTGAGTATGGTTGGACTACTCAGAAGGTGTTTCATCTTATGAACTTTGTCGTCAATGGAG
upper sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S237_67V6.1 (Physcomitrella patens), 3'ss of exon 1
gaattgtttttcactgtcgtg-atttg-tggagttgagcttgat-tgttgagaaat--cttatgttg--tgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
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-------ttcacattgtggtatacctgctttggtagcactcaatctcctgccaagtttctcttcttggttgtgaatggacttgacatcaagtgttgggaatgtgcagGTGCAACTGATACGGATAGAACTGAGAGTTCCGGAGTACGGGTGGACTACTCAGAAAGTCTTCCATCTGTTGAACTTTATTGTAAATGGAG
upper sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S295_28V6.1 (Physcomitrella patens), 3'ss of exon 1
gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatct-tatgttgtgcggtt----gactaagatttcattga-----tgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
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---------tgtactgt-atgagcgaggcattgaagatttttcaatacagaacctctatattgtgttcttcggtgcatacatgtacatcaagtgtgtttggaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACACAGAAAGTCTTCCATCTCTTGAATTTCATCGTTAATGGAG
upper sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
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-----------------------gtatggaatccggctagtttgttgg----tctt---ttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAGMapped 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|161706415|gb|FC057579.1|FC057579EST: TCTTCTACGCTCTCTGTGGTGCTTATGCCCTAGTTTCTTCAGTTGCTCTG ATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACG
genomic: TCTTCTACGCTCTCTGTGGTGCTTATGCCCTAGTTTCTTCAGTTGCTCTGgtactctttc ... cactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
cattgat putative branch site (score: 4)
aatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
- - - - - - - - - - - -ttgtgga
- - - - - - - - - - - - - - - - -gagcttg
- - - - - - - - - - - - - - - - - - - - - - - -agaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg