Sequence
atgc intronic sequence ATGC exonic sequence...ttggagatatttagtttagttataattcagtgccaaaccattttgaaggtcttttgatttgcattctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 8
---ttggagatatttagtttagttataattcagtgccaaaccattttgaaggtcttttgatttgcattctcttgagaacttat-ttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
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cattgagaaaagcattgccgacttactggtttttgaagtctggaaatcatagtttgcggagttatatt----taaggtttcatattttctatcacgtggcacagGTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG
upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
-----ttggagatatttagtttagttataattcagtgccaaaccattttgaaggtcttttgatttgcattctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
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catgtttgggaatagc-agttggttctaagcttggcatcctagtggtt----aatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 7
-ttgg--agatatttagttta-gttataattcagtgccaaaccattttgaaggtcttttgatttgcattctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
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tttagctataaatccaacggacatcagaaatcattgacaaagtatttcca---ctttataatctattatcatttctcacatttttctttt-ctatgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGAGGCTCAAG
upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 7
------ttggagatatttagtttagttataattcagtgccaaaccattttgaaggtcttttgatttgc-attctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
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gtttacctataaatccaagggaca-tcagaaatcattgacaaagtatttcca---ctttataatctattattgtttctcagatttttttttctacgattt---ttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGCGGCTCAAG
upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 8
ttggagatatttagtttagttataattcagtgccaaaccat----tttgaaggtcttttgatttgcattctcttgagaacttatttttg---tgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
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--gtaagctctatctatagttatactcttatactcgtatgtattctttgaagccttcagcatatgttgagcgatgaaaatgattgtttgagttgttgtggatttaagGTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAG
upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ25923 (Selaginella moellendorffii), 3'ss of exon 7
ttggagatatttagtttagttataattcagtgccaaaccattttgaaggtcttttgatttgcattctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
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------------------------------------------------gtgagtcaatctc--ttcctttgaagctgtgttaactggcctttatgcgcagGTGTTTGGAACATTCGCTACATCAGGCTCTGATGGTGCTTTTAACTTCTGGGACAAGGACAGCAAGCAGAGGCTCAAGMapped 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|110386126|gb|EC950701.1|EC950701EST: ACAGGGAAGGCAATGAGATATACTCAGTGAACTCTCTAAACTTCCATCCT GTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGG
genomic: ACAGGGAAGGCAATGAGATATACTCAGTGAACTCTCTAAACTTCCATCCTgtaagattct ... cttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGG
EST:
gi|351043163|gb|FQ451336.1|FQ451336EST: ACAGGGAAGGCAATGAGATATACTCAGTGAACTCTCTAAACTTCCATCCT GTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTTG
genomic: ACAGGGAAGGCAATGAGATATACTCAGTGAACTCTCTAAACTTCCATCCTgtaagattct ... cttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCT-G
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggtcttttgatttgcattctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
ttttgat putative branch site (score: 4)
tttttgtgcctctt putative PPT
aacttattttt 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
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ttggagatatttagtttagttataattcagtgccaaaccattttgaaggtcttttgatttgcattctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG
- - - - - - - - - - - - - - - - -caaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc