Sequence
atgc intronic sequence ATGC exonic sequence...tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 5
-----------------------------tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
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gttggtgcattaatttcaataggtttctatctgtttgctcattcatgataaaaatttatacagcaagctta-acttgcttgggcct-tgcttttagtatttgttcattcatgtta-cttcgaattgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 5
-----------------------------tatattatattatttaggaaataaattgtggtatgaagca-aatgagtacacacc---cttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
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gttggtgcattaatttcaatagatttttatctgtttgctcattcatgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgttcattcatgattcatgttacttcgaactgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
-----tatattatattatttaggaaataaattgtggt--atgaagcaaatgag--tacacacccttgtggaatcagtattcatcttcttct----gttaactgttctcta----cagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
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gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
-tatattatattatttaggaaataaattgtggtat--gaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
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ggattttgatctagataa-aattatataggtgtactggcagctgactcattgaaattgaatctttttcagaagctaa-tggttttactgattattctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G41070.3 (Glycine max), 3'ss of exon 5
-----tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
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gattttgatctagataaaatcatataggtgtactggtagctgactcattgaaattgaatcttgt----tcagaagctaa-tgattttactgattattctttgcagACCTGGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAGG
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
-tatattatattat--ttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
|| |||||| | || ||| | || | || | | | || | |||| ||| | | ||| | |||| | |||| | || ||||||||||||||| |||| |||||||| || |||||||| || ||| |||| ||||||||||||| |
caatcttatatctccacttggcaatgtgtaatg-tgtgttgtcatttgctattttggataaaagaattgatatcaggtaccattgatta--tattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
--tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
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caagcaactcatctttcacctggcaatgtgtaatgtgcgttatctt--cccttattttggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgt--------ggaatcagtattcatcttcttctgt-taactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
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gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatatt-ttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGGMapped 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|33405593|gb|CF211220.1|CF211220EST: TTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG AGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATA
genomic: TTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACGgtaattattc ... ttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATA
EST:
gi|29781753|gb|CB346482.2|CB346482EST: TTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG AGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATA
genomic: TTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACGgtaattattc ... ttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
tgttaac putative branch site (score: 2)
ctgttctct CT-rich tract
tattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - aaataaa
- - - - - - - - - - - - -ttgtggt
- - - - - - - - - - - - - - - - - -aagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - caccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaatca