Sequence
atgc intronic sequence ATGC exonic sequencegtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC
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----------------------------------------gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaa-actataac-----cttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
upper sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G412899_T05 (Zea mays), 3'ss of exon 9
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgtattcactgattccttt-tgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC
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--------------------------------------------------gtacaagctgttctatatcctttttgttgtgtttatggacttctaataacctgagttcagtctgtctgtgaagtttgttcattacaagttccttttttggtacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCC
upper sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G09270.3 (Glycine max), 3'ss of exon 9
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttc-ttattctccttttgcctccaagaat-gctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC
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--------------------gtatgcattt------ttcctggtttgtctctgggatagttgtgacttg-tgagtgtatttgccattgttgttatctggtcactggtttccttaggtttccaaaagttattttttattcacaagttcgttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAATGCTGTGTTTTATTTCTCTTCAACTGTTTTTAAAAGTGCTGGAGTGCC
upper sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 9
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC--------------------------------------------
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---------------------------------------------------------------------------------------------------------------------------------------------------------------tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG
upper sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgt-attcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC
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----------------------------------gtatgtagaactctttgcttttgtcccgcgga--aggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtat-----agtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACCMapped 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|110715750|gb|EE094159.1|EE094159EST: GATAGATGCTGTGAAGCTCTCAGAATTGCTTTATGGGCGTCATTTCAGAG TTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAA
genomic: GACAGATGCTGTGAAGCTCTCAGAATTGCTTTATGGGCGTCATTTCAGAGgtagatatga ... ccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAA
EST:
gi|110399825|gb|EC966355.1|EC966355EST: GACAGATGCTGTGAAGCTCTCAGAATTGCTTTATGGGCGTCATTTCAGAG TTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAA
genomic: GACAGATGCTGTGAAGCTCTCAGAATTGCTTTATGGGCGTCATTTCAGAGgtagatatga ... ccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAA
EST:
gi|161711472|gb|FC058674.1|FC058674EST: GACAGATGCTGTGAAGCTCTCAGAATTGCTTTATGGGCGTCATTTCAGAG TTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAA
genomic: GACAGATGCTGTGAAGCTCTCAGAATTGCTTTATGGGCGTCATTTCAGAGgtagatatga ... ccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttattctccttttgcctccaagaatgctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC
cactgat putative branch site (score: 3)
ttccttttgc CT-rich tract
tttgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT