Sequence
atgc intronic sequence ATGC exonic sequencegtacgttagggttttcttaacgcggctcagatctgagtgatctgtgcgtatttggttcgggatggtgggttggatgcggatctcggttgatgtctttttgtttttgtttggtttggtttggttcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGAAGGCCCTCGATGCCCTAATTGCTTTTCTGAAAGCTGCCGACGCTGATGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------gtacgttagggttttcttaacgcggctcagatctgagtgatctgtg-cgtatttggttcgggatggtgggttggatgcggatctcggttgatgtctttttgtttttgtttggtttggtttggttcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGAAGGCCCTCGATGCCCTAATTGCTTTTCTGAAAGCTGCCGACGCTGATGC
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gtgagataagctcccggtggctcccgatccacgcccattgcgcgctcggatccgc---gccctgcttgattctcgctgtttcgtctcgttttttttttcgaggggtgttttagcgttagatctga----aggcccttttgtcttt-tccg--ccggt---ggttagGGCCGTTGTTTAAGAAGACTGTGGCGGATTCGAACGCGCCGGTGCAGGAGAAGGCGTTGGATGCCCTGCTCGCTTTCCAGCGGGCGGCTGATGCTGATGC
upper sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 1
-----------------gtacgttagggttt-tcttaacgcg-gctcagatctgagtgatctgtgcgta-tttggttcgggatggtgggttggatgcggatctcggtt-gatgtct----ttttgtttttgtttggtttggtttggt--tcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGAAGGCCCTCGATGCCCTAATTGCTTTTCTGAAAGCTGCCGACGCTGATGC
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gtgagatacctccccctacgcctcccgatccgccccatttcgcgctcggatctgcgctatgctcgattagcgcggtaccgtttggggatttcaaatcatttttgggctcaagatctgaagtctagtgtttttctgttctactccgatggttagGGCCGTTGTTTAGGAAGACGGTTGCAGATTCCAATGCGCCGGTACAGGAGAAGGCGCTCGATGCCCTTCTCGCGTTCCAGCGAGCTGCTGACGCCGATGC
upper sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G070126_T01 (Zea mays), 3'ss of exon 1
-----------------gtacgttagggttt-tcttaacgcg-gctcagatctgagtgatctgtgcgtatt-tggt-tcgggatggtgggttggatgcggatctcggttg--atgtct----ttttgtttttgtttggtttggtttggt--tcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGAAGGCCCTCGATGCCCTAATTGCTTTTCTGAAAGCTGCCGACGCTGATGC
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gtgagataccttcccctacgcctctcgatccgccccatctcgcactcggatctgcgctatgctcgattagtgcggtaccgtttcggggatttcaaatcattttttgggtgcaagatctgaagtccattgtttttctgttctactccggtggttagGGCCGTTGTTTAAGAAGACGGTTGCAGATTCCAATGCGCCGGTACAGGAGAAGGCGCTCGACGCCCTTCTCGCGTTCCAGCGAGCTGCTGACGCCGATGCMapped 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|34549765|gb|CF517997.1|CF517997EST: CGTCTGCGACTCCATCACGGATCCCAAAGATCCTCGCCTCCGTGAATTCG GTCTGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGA
genomic: CGTCTGCGACTCCATCACGGATCCCAAAGATCCTCGCCTCCGTGAATTCGgtacgttagg ... tttggttcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGA
EST:
gi|34550714|gb|CF518932.1|CF518932EST: CGTCTGCGACTCCATCACGGATCCCAAAGATCCTCGCCTCCGTGAATTCG GTCTGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGA
genomic: CGTCTGCGACTCCATCACGGATCCCAAAGATCCTCGCCTCCGTGAATTCGgtacgttagg ... tttggttcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatgcggatctcggttgatgtctttttgtttttgtttggtttggtttggttcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGAAGGCCCTCGATGCCCTAATTGCTTTTCTGAAAGCTGCCGACGCTGATGC
ggttgat putative branch site (score: 5)
tttttgtttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttagggttttcttaacgcggctcagatctgagtgatctgtgcgtatttggttcgggatggtgggttggatgcggatctcggttgatgtctttttgtttttgtttggtttggtttggttcagGTCCGTTTTTCAAGAAGGCTGTTGCGGATTCGAATGCGCCGGTTCAGGAGAAGGCCCTCGATGCCCTAATTGCTTTTCTGAAAGCTGCCGACGCTGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT