Sequence
atgc intronic sequence ATGC exonic sequence...ggtagtaaatggtactactatatattttctcataggtcacactgacagctgagtttaatttgttcttacaccactgactgaatatgctgcatatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 8
-ggtagtaaatggtactactatatattttctcataggtcacactgacagctgagtttaatttgttcttacaccactgactgaatatgctgcatata-tgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA
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actttgcagtaggatctac-attggtttttggatgtataaacaagatggccttattacaacggagcgttt-ccattggttaatctatttttatgcaatacagGCACTCAAGAAGAAGCAGCAGAGGCATACGACATTGCTGCCATCAAGTTCCGTGGCCTGAACGCGGTGACGAACTTTGACATCACAAGGTACGACGTGGA
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------ggtagtaaatggtactactatatattttctcataggtcacactgacagctgagttt----------aatttgttc---ttacaccactgactgaatatgctgcatatatg---cagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA
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gtaagtgcaggtctcacatgaattcgtgcacagtagcggattactctcgctccatatagcggtcatttctcctgataggacttccgacgttgcttccagagacgtcggagtgttctggatctagatgtgcccatgttatctaaatgtttgaataaactggctgtgtaattcagGCACTCAAGAGGAAGCAGCGGAGGCCTACGACATAGCTGCCATAAAATATCGTGGAATTAATGCCGTCACAAACTTTCATATCTCTCGTTACCTAGCTAA
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 7
ggtagtaaatggtactactatatattttctcataggtcacactgacagctgagtttaatttgttcttacaccactgactgaatatgctgcatatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA
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-------------------------------gtaagttct--cagttgtttaaagcaatgcaatgcctcgct-cggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTCAA
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 7
ggtagtaaatggtactactatatattttctcataggtcacactgacagctgagtttaatttgttcttacaccactgactgaatatgctgcatatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA
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-------------------------------gtaagttct--cagttgtttagagcaatgcaatgcctcgct-cggtctgatcttgtttaaaccaaccagGCACGCAAGAGGAAGCCGCGGAAGCATACGACATCGCCGCGATCAAGTTCCGGGGCATCAACGCGGTCACCAACTTCGACATCAGCCGCTACGACCTTAAMapped 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|101388676|gb|EB816323.1|EB816323EST: TCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCA CAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCC
genomic: TCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCAgtaagaaaag ... atatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCC
EST:
gi|94479778|gb|EB708736.1|EB708736EST: TCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCA CAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCC
genomic: TCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCAgtaagaaaag ... atatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagctgagtttaatttgttcttacaccactgactgaatatgctgcatatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA
cactgac putative branch site (score: 2)
tttaatttgttctta 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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ggtagtaaatggtactactatatattttctcataggtcacactgacagctgagtttaatttgttcttacaccactgactgaatatgctgcatatatgcagCAACTCAAGAAGAAGCAGCCGAGGCGTACGACATAGCGGCCATCAAGTTCCGCGGCCTGAACGCGGTGACGAACTTCGACATAGCAAGATACGACGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA