Sequence
atgc intronic sequence ATGC exonic sequence...tgggttccaaacttccttcacctttctaatcatggaagaactagtgataacaacaaattttttccactgtgcttttaactgacggatgtatgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCTCGCAATGCACACCCTCCAGAGCCAGAAGGTTATGATGGTACTGAAGTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g70100.1 (Oryza sativa), 3'ss of exon 2
tgggttccaaacttccttcacctttctaatcatggaagaac-tagtgataacaacaaattttttccactgtgcttttaactgacggatgtatgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCTCGCAATGCACACCCTCCAGAGCCAGAAGGTTATGATGGTACTGAAGTTG
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catgtacataattgtctttgt-ttggtaaacagaaaagtgtataagtgtatatatgtatacattcagacttaccactttaggaatttctggcatatttcagGACTTGAGCCTTCTACTTCTCACTTCTGGTAGGGATCCAGGTATAATACCTCGGAATGCACACCCTCCAGAACCTGAAGGTTTGGATGGCAATGCAGAGG
upper sequence: Vv17s0000g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G433942_T01 (Zea mays), 3'ss of exon 2
-tgggttccaaa-cttccttcacctttctaatcatggaagaactagtgataacaacaaattttttccactgtgcttttaactgacggatgtatgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCTCGCAATGCACACCCTCCAGAGCCAGAAGGTTATGATGGTACTGAAGTTG
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atacataaaaaaattttatctgaagtcatgatcatgctggtaaagagaatatatacaaaacataccctctaacttgtttaagcatt-atgccacctttcagGATCTGAGT-CTTCTGCTTCTAACTTCTGGGAGAGATCCAGGGATCATACCTCGCAATGCACATCCTCCAGAACCCGAAGGGTTTGATGGCAATGCAGAGG
upper sequence: Vv17s0000g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G034833_T02 (Zea mays), 3'ss of exon 2
tgggttccaaacttccttca-cctttctaatcatggaagaactagtgataacaacaaat--tttttccactgtgcttttaactgacggatgtatgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCTCGCAATGCACACCCTCCAGAGCCAGAAGGTTATGATGGTACTGAAGTTG
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-cgtacacaaattatcttcagtcatggtcgtgctggtaaagagaa-gaaaacagagaatgatcatcccatctaacttgtttacgcattatgccacctttcagGATCTGAGT-CTTCTGCTTCTAACTTCTGGGAGAGATCCGGGGATCATACCTCGCAATGCACATCCTCCAGAACCTGAAGGGTTTGATGACAATGCAGAGG
upper sequence: Vv17s0000g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G01290.1 (Glycine max), 3'ss of exon 2
tgggttccaaacttccttcacctttctaatc----atggaagaactagtgataacaacaaattttttccactgtgcttttaactgacggatgtatgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCTCGCAATGCACACCCTCCAGAGCCAGAAGGTTATGATGGTACTGAAGTTG
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--gagtgaaaattgatgcgactattgagatcttttacatcacaatctttctcattcaccactgtactcccaagtcataataactcttgaa-atgtattctc-agGTTCTGATCACCCTTGTAGTGACCTCTGCAAGAGATCCTGGCATAGTACCTCGTAATGCCCAGCCTCCGCAGCCAGATGACCATCATGGGACTGATAATAMapped 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|161721421|gb|FC071075.1|FC071075EST: ATCACTTGGGAATATCAATAATGGTTGTTGTAATCGCATTCACATTATAT ATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGTATAATACCT
genomic: ATCACTTGGGAATATCAATAATGGTTGTTGTAATCGCATTCACATTATATgtgagcccta ... tgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataacaacaaattttttccactgtgcttttaactgacggatgtatgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCTCGCAATGCACACCCTCCAGAGCCAGAAGGTTATGATGGTACTGAAGTTG
aactgac putative branch site (score: 2)
tgttttcc putative PPT
aacaaatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggttccaaacttccttcacctttctaatcatggaagaactagtgataacaacaaattttttccactgtgcttttaactgacggatgtatgttttccagATCTTAGTTCTTCTTCTGCTAACCTCTGGAAGAGATCCTGGCATAATACCTCGCAATGCACACCCTCCAGAGCCAGAAGGTTATGATGGTACTGAAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - ccaaact
- - - - - - - ccttcac
- - - - - - - - - - - - - - - - -ggaagaa
- - - - - - - - - - - - - - - - - - - - - - - - -acaacaa