Sequence
atgc intronic sequence ATGC exonic sequencegtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 3'ss of exon 4
------gtataatggccata-tatggacataaatt---tgttttgcaacttcaattagaataat---gttctaa--tttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
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gcaagtttgaaatttctgtaactctgatttagattttatgttcatcatttgtattctcagtatttgaattgtaaggctcaaaatgttcgcatgcacta--ctgttacagAGGACGCTCCTGGCTATGCCAGAAAATGGTATTGGCTTGTTCCCGGACGTTGGCTTTGCTTACATTGGTGCCAAAGCTCCAGGAGGTGGTGCTGTTG
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G047564_T02 (Zea mays), 3'ss of exon 4
gtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
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--gcaattttttgtctccaatttatgtttgtttt-taatttca-ttatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTG
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G047564_T01 (Zea mays), 3'ss of exon 3
gtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG---
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--gcaattttttgtctccaatttatgtttgtttt-taatttca-ttatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTGGTA
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G04460.1 (Glycine max), 3'ss of exon 4
gtataatggccatatatggacataaatttgttttgcaact-tcaattagaataat-gttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
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-----gtatgctcacctggcaatagttgtctcgtttagtcatgaattgccgttgtagatcctatttatgacttttctttttcattcacatttatagAGAACTGTTCTTGCGATGCCAGAAAATGGAATTGGTTTGTTCCCAGATGTAGGTTTTGCTTATATAGCGGCTCAAAGTCCAGGGGAAGGATCCGTTG
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G35260.1 (Glycine max), 3'ss of exon 4
gtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgata----tttatttgtactaatttgttt-cagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
| | |||| ||| ||| | | ||| | | | ||| ||| | ||||| ||| ||| | | || ||| ||||||||| ||||||| |||||||||||||||||||| ||||| || ||||| || |||||| | ||||| || || |||||||| |||||||| ||||
-----gtatgctcgcatggcaatag--ttgcctcgtttagtca--tgaattgctgtgctagatcctgattgaccttttttttttcaaacacatttacagAGAACTGTTCTTGCGATGCCAGAAAATGGAATTGGTTTGTTCCCTGATGTAGGTTTTGCTCATATAGCGGCTCAAAGTCCAGGGGAAGGATCCGTTG
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ14541 (Selaginella moellendorffii), 3'ss of exon 4
gtataatggccatatatggacataaatttgttt-tgcaacttcaattagaataatgttctaatttctgatatttatttgtactaatttgtt-tcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
|| | || || | | | | | ||| || | | | | ||||| ||||| |||||| || ||||||||||||| || |||||||| |||||||||||||| ||||| ||||| || |||||||| | | ||| | | | ||| | || |
-----------------------------gtctgtggcgttttaccttggctcgt-ttcgaagctaagctttgcgtttgt-----tttgtgatcagAGGACGGTTCTTGCCATGCCTGAGAATGGAATCGGCTTGTTTCCAGACGTTGGTTTTGCATATATAGCAGCTCGAACTCCTGCAAATGGAGCTGTAG
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ26244 (Selaginella moellendorffii), 3'ss of exon 4
gtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgatattta--tttgtactaatttgtt-tcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
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-----------------------------------------------gtctgtggtggctcgtttcgaagctaagctttgcgtttttttgtgatcagAGGACGGTTCTTGCCATGCCTGAGAATGGAATCGGCTTGTTTCCAGACGTTGGTTTTGCATATATAGCAGCTCGAACTCCTGCAAATGGAGCTGTAGMapped 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|110699628|gb|EE076795.1|EE076795EST: ATGGTCGTTACCGGATTGTCACAGAG AGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTT
genomic: ATGGTCGCTACCGGATTGTCACAGAGgtataatggc ... tttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTT
EST:
gi|161717741|gb|FC066584.1|FC066584EST: GTTTTGGAATTGGACTGTCTGGTCATGGTCGCTACCGGATTGTCACAGAG AGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTT
genomic: GTTTTGGAATTGGACTGTCTGGTCATGGTCGCTACCGGATTGTCACAGAGgtataatggc ... tttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTT
EST:
gi|110399519|gb|EC966027.1|EC966027EST: GTCATGGTCGCTACCGGATTGTCACAGAG AGAACTCTTCTTGCCATGCCAGAAAATGGAATGGGCTTGTTTCCAGATGTT
genomic: GTCATGGTCGCTACCGGATTGTCACAGAGgtataatggc ... tttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaattagaataatgttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
tactaat putative branch site (score: 1)
tttgtttc CT-rich tract
aataatgttctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA