Sequence
atgc intronic sequence ATGC exonic sequencegttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 3'ss of exon 3
gttag-aaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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gttagcatgtagcttgttttatacctgctttttgcacgagatttttgt-atccgagttgagtaatagcctagttttttttttaataaaaaagtaatagcctagtttga-atggtgaaaa-------tgcagATGTGTACTCGAACCAGGTGACAAAATTGTTGATTGCCCTCCAACTTTTACGATGTATGAGTTTGATGCGTCAGTCAATGGTGCACTTGTGATCAAGG
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G170595_T01 (Zea mays), 3'ss of exon 3
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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-------------------gttagtgtctgtatctcaagactcca---actttttgctgatatcttcatccaaaggctg--agtt----atcgtctatttcataaatggcggaattg----------cagATGTGTGCTTGAACCAGGCGACAAAATTGTTGATTGCCCTCCAACATTCACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
gttagaaatggaagattttgtgttt-acttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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gttagaaccaataccttatgtattttagataagcctcaaattctttctcttcat--gctaattgtcatcat--agctacgacaatcacca-tcatacatgcttctcata------------tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S175_129V6.1 (Physcomitrella patens), 3'ss of exon 4
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattat-tgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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------------------------tccgtggtatcagctttcatgacggttcttggtgtttctgagatctttagttgtct---ttctgaattg--aagtgtccttggcatgtgattcggtctcaa--acagGTGTACATTAGATCCTGGTGACAAGATATTGGACTGTCCACCCACATTCACTATGTATGCATTTGACGCTGCAGTGAACGGAGCTTCTGTCATCAAAG
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ04408 (Selaginella moellendorffii), 3'ss of exon 2
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattac---agATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG--
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---------------------------------------------------gtaagtgaccaactcctagcgtgtttt------ttcttttttcttcttttgctcttcacgagatggttcttcatctctttagTTGTACATTGGAAGGTGGTGACAAGATTGTGGATTGTCCTCCCACTTTGACAATGTATGCGTTTGATGCCGCTGTAAGCGTCATCAAAGGTCTTGTTTGT
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ31554 (Selaginella moellendorffii), 3'ss of exon 1
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgta-gtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattac---agATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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-----------------------------------------------------------gtaagtgaccgactcctagcgtgttttttctttttcttcttttgctcttcacgagatggttcttcatctctttagTTGTACATTGGAAGGTGGTGACAAGATTGTGGATTGTCCTCCCACTTTGACAATGTATGCGTTTGATGCCGCT-------------------------
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ31551 (Selaginella moellendorffii), 3'ss of exon 3
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattac---agATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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--------------------------------------------------------------gtaagtgaacgactcctagcgtgcttttttttttcttttgctcttcacgagatggttcttcatctctttagTTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAG
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ04411 (Selaginella moellendorffii), 3'ss of exon 3
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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----------------------------------------------------gtaagtgaccgactccttgcgttttttttttttttcttttccttttgctcttcacgagatggttcttcatctctttagTTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAG
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ38596 (Selaginella moellendorffii), 3'ss of exon 3
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattac---agATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
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---------------------------------------------------gtaagtgaccaactcctagcgtgtttt------ttcttttttcttcttttgctcttcacgagatggttcttcatctctttagTTGTACATTGGAAGGTGGTGACAAGATTGTGGATTGTCCTCCCACTTTGACAATGTATGCGTTTGATGCCGCTGTAAGC-------------------Mapped 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|71857670|gb|DT006725.1|DT006725EST: TATATTCTTGCCGGATGTGGTGCAGATGAGCTCATTGATTTGATTATGCG ATGTGTACTGGATCCTGG
genomic: TATATTCTTGCCGGATGTGGTGCAGATGAGCTCATTGATTTGATTATGCGgttagaaatg ... tctattacagATGTGTACTGGATCCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
cattgac putative branch site (score: 3)
cctctatt CT-rich tract
aattgtttattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaaatggaagattttgtgtttacttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT