Sequence
atgc intronic sequence ATGC exonic sequencegtagttatttgatgaactggattcttcactctcttgttaatcattatagtcaataaatgacatatttgttcttgttgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g34000.1 (Oryza sativa), 3'ss of exon 4
--------gtagttatttgatgaactggat-tcttcactctcttgttaatcattatagtcaa--taaatgacatatttgtt-cttgttgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
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gtaaaaatccaattatcatctgattttgatgtattcaaccatacattattcttccccaatgatttaatttctttatttaaaatttcatgctatacagTTTTCGAAGGAGCGACGTAGTATTATTCCTGCTGGAGATACTTCACAATTCATTTCCTCGAGTGAAGCTGATATAGCAATTTTGGAAGAACCAGAGCATC
upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 4
gtagttatttgatgaactggattcttcactctcttgttaa--tcattatagtcaataaat-gacatatttgttct-tgttgtttctt--agTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
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------------gtaact--atcatacatttttttgtcaaggtgcatatcttgaataactcaactgatatgctgtatgccgtaccctgcagTTCTCCAAAGAGCGCCGTAGCATCATTCCTGCTGGGGATACATCACAGTTCATTTCATCGAGAGAAGCTGATATAGCAATATTGGAAGAACCAGAGCATC
upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 2
gtagttatttgatgaactggattcttcactctcttgttaatcattatagtcaataaat-gacatatttgttcttgttgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
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---gttacatt-taatgtgtattatgtcaaatactcaaattcgatattttcaatgacttgatattgacatgttatatgttttacagTTCTCAAAAGAGCGGCGTAGCATCATTCCAGCTGGTGATACGTCTCAGTTCATACCGTCAAGAGAAGCTGATATAGCAATATTGGAAGAACCAGAACATC
upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G092588_T02 (Zea mays), 3'ss of exon 2
--gtagttatttgatgaactggattcttcactctcttgttaatcattatagtcaataaat-gacatatttgttcttgttgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
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gcaaggttacatt-taatgtgtattatgtcaaatactcaaattcgatattttcaatgacttgatattgacatgttatatgttttacagTTCTCAAAAGAGCGGCGTAGCATCATTCCAGCTGGTGATACGTCTCAGTTCATACCGTCAAGAGAAGCTGATATAGCAATATTGGAAGAACCAGAACATC
upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 5
gtagttatttgatgaactggattcttcactctcttgttaatcattatagtcaataaatgacatatttgttcttgttgtttct-tagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
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gtaactcttcctt--------ttttcagcacaatgcttgaacactat-gtgcatagctcacgtagtcgcaatttttccaactacagTTTCAAAAGGAAAGGAGAAGCATAATTCCTGCTGGGGACACTTCACAGTTCATACCATCAAAGGAAGCTGATATTGCAATCTTGGAAGAGCCCGAGCACC
upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 4
gtagttatttgatgaactggattcttcactctcttgttaatcattatagtcaata--aatgacatatttgttcttgttgtttct-----tagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
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gtaacttaatgagaaagttagctataatcctttatgtcatactttcatatcactactgtcagttcttatgtttttgtcattctcatgtgtagTTTTCGGAAGCAAGGCGGAGTATAATACCTGCTGGAGATACTTCTCAATTTATACCATCCAGGGATGCTGACATTGCTATCCTGGAAGAACCAGAACATT
upper sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 4
gtagttatttgatgaactggattcttcactctcttgttaat--cattatagtcaataaatgacatatttgttcttgttgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
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gtaactttttggtaaagttagctatttcctttatgtttcatatcactactgtcggttctt-acat-tttgaaattctcatgtgt-agTTTTCGAAAGCAAGACGGAGTATAATACCTGCTGGAGATACTTCTCAATTTATACCATCCAGGGATGCTGACATTGCTATCCTGGAAGAACCAGAACATTMapped 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|219555374|gb|FG984547.1|FG984547EST: AAAGGGTTGGTTTTAAGGCTGATTTCAAGATCTCCTTTTATCCAGGAAAG TTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTT
genomic: AAAGGGTTGGTTTTAAGGCTGATTTCAAGATCTCCTTTTATCCAGGAAAGgtagttattt ... tgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTT
EST:
gi|110725725|gb|EE102558.1|EE102558EST: CTTTTATCCAGGAAAG TTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTT
genomic: CTTTTATCCAGGAAAGgtagttattt ... tgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttgttaatcattatagtcaataaatgacatatttgttcttgttgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
tgttaat putative branch site (score: 3)
ttcttgttgtttctt putative PPT
ttaatcattatagtca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttatttgatgaactggattcttcactctcttgttaatcattatagtcaataaatgacatatttgttcttgttgtttcttagTTTTCAAAATCTAGGCGGAGTATTATACCTGCTGGAGATACTTCTCAGTTTATTCCATCAAGGGATGCTGATATTGCAATCCTGGAAGAACCAGAACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC