Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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gtaagcacctagatttatcccattcattgctgttgcctcgtgttc-ctcat-------catttgtgtttatgtattaaaagtaataacatcat-taacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g57940.2 (Oryza sativa), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaa-cagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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------------gtaagtttcgga-tcacctttttgcattgac---cacctgattttat-tactcctcactgaaaataacagcattggaacttgcaaacagGATGTCTGCCCATATGGTTGCTTGCATTGCTGTGGAAGCGATATCAATTCTTGAGAAGCTTCACTCTAAAGG
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 6
gtaagaaatagaatctctctctctctct-ctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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-------gtaagatgacatgttctgtctgctttgtttaactcatgttattctaagcagctgactgatcaccaatatttgatt----------------cagGATGACACCTAATATGGTTGCTTGCATTGCTGTAGAGGCAATTTCTATACTTGAGAAACTTCATGCAAAAGG
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 4
-------------------------------------gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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ggtatgttgtttatggtatttcagctgtatttaattcgatggggcaggcataagtatcttccattcttttttatg---gtatcttttgtcactcatgtatcagCTTCTAGACTAAACGAGTCAACAATCTCAAACAGGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCAATTCTTGAGAAGCTCCATTC------
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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-------gta-agtatcttccattctttttaa-tggtatcttttgtcactcatgta------tcagcttctagactaaacgagtcaacaatctcaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCAATTCTTGAGAAGCTCCATTCTAAAGG
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaa-cagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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------------gtaagtatcttccattcttttttatg-atat-cttttgtcactcatcagcttttagact------aaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacac-----acacacacacacaagtggacattttttttcctgtttttaatt--tatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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gtaagatttgtaccctcccttttgttagtataggttcacttttaatagctgcaatttatttaaactcttcctatataagccccattaacattttagttctg-gacagAATGTCACCAAATATGGTTGCGTGCATTGCAGTAGAGGCAATATCAATTCTTGAGAAGCTCCACTTGAAAGG
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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---------------gtaagcactcttctcctctcac-cacacttccttctgattgcaagattcttgatttgattcatgttcgt----gtcatgtggcagGATGTCTCCAAACATGGTAGCCTGCATTGCAGTTGAGTCCATATCTATTCTTGAGAAACTTCATATGAAAGG
upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
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gtaagtact----tttatcattctatattttcttaccaaccatgctcatgcagat--atgctaaatttattattttt---ctatttgg---------tagGATGTCTCCAAACATGGTAGCATGCATTGCAGTGGAGGCGATATCTATTCTTGAAAAACTGCATATGAAGGGMapped 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|71861339|gb|DT010394.1|DT010394EST: ACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGAC GATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCT
genomic: ACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGACgtaagaaata ... cctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCT
EST:
gi|110385816|gb|EC950372.1|EC950372EST: GACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGAC GATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAA
genomic: GACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGACgtaagaaata ... cctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
ttttaat putative branch site (score: 3)
acattttttttcctgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC