Sequence
atgc intronic sequence ATGC exonic sequencegttttttttctcatgctatcttttattaattgttttgtgctgtattatttggtgttgattttcatgttagacggacaattatacttgaatcagGCCGGGATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCGACAGACCAAGAGATTCTTGAACACTTAGAGGCAAAGGTGCTGTCTGATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g00350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------------------------gttttttttctcatgctatcttttatta-attgttttgtgctgtattatttggtgttgattttcatgttag--acggacaattatacttgaatcagGCCGGGATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCGACAGACCAAGAGATTCTTGAACACTTAGAGGCAAAGGTGCTGTCTGATA
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gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatatatactgcgtagtactacattaattcttcttttggt-tgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC------
upper sequence: Vv10s0003g00350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G134717_T01 (Zea mays), 3'ss of exon 1
gtttttttt--ctcatgctatct--tttattaattgt-tttgtgc-tgtattatttggtgttgatttt-------catgttaga---cggacaattatactt-----gaatcagGC--CGG-GATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCGACAGACCAAGAGATTCTTGAACACTTAGAGGCAAAGGTGCTGTCTGATA
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gttacccacaccacacgccatctagctagctagctacattcatgcatggaatggacgacaccactcactcacacgcacgctagcgatcggatcgtcgtccatcagGTGCAGCAGGCGGCGGCGATCCAGGACCTGCCGGGGCTGCCGGCGGGCGTGAAGTTCGATCCGACGGACCAGGAGCTGCTGGAGCACCTGGAGGGGAAGG------------Mapped 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|26267025|gb|CA818088.1|CA818088EST: CGACACTAACATGCCCTTCATGTGGCCACCAAATAGAATTCCAAGATCAG GCCGGGATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCG
genomic: CGACACTAACATGCCCTTCATGTGGCCATCAAATAGAATTCCAAGATCAGgttttttttc ... cttgaatcagGCCGGGATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgtattatttggtgttgattttcatgttagacggacaattatacttgaatcagGCCGGGATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCGACAGACCAAGAGATTCTTGAACACTTAGAGGCAAAGGTGCTGTCTGATA
tgttgat putative branch site (score: 4)
aattatacttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttttttctcatgctatcttttattaattgttttgtgctgtattatttggtgttgattttcatgttagacggacaattatacttgaatcagGCCGGGATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCGACAGACCAAGAGATTCTTGAACACTTAGAGGCAAAGGTGCTGTCTGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG