Sequence
atgc intronic sequence ATGC exonic sequencegtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 1
--------------------------------gtaagctactcccggcctttcccgcgataggcgg--tgtttgtgggaatctagtatctgatctgtgcg-----cac-----tttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
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gtaagacgctcctcgtcgccgttgctggatcccccagatgagctagggattttatggtagggttagatttttttttcgtgggtggcttctgattcgtgtggtttccgccttcgttttcagTTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT
upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 1
-----gtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT-----------------------------------
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gtgttgtctctaaaccctaattgcttccctgtttg--gatttttgtgtgtttatcgc-tgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCTGTAATCATTTCACTCTCTCTTCAATTTTCATTTGT
upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
-----gtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
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gtgttgtctctaaaccctaattgcttccctgtttg--gatttttgtgtgtttatcgc-tgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
---------------gtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
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gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattgggactaatta-tgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT
upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G24630.1 (Glycine max), 3'ss of exon 1
-----gtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
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gtgttgtctctgaaccctaattgcttccgtgtttg--gatatttgtgtgtttgtcgc-tgaaacatgttcggttttgctgcagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT
upper sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S253_7V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------gtaagctactcccggcctttcccgcgataggcgg--tgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
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gtacacgcatacgggggctccctctgccctcccctgtttcctttccatcttcacatgccaatcttcgcattcactgctctctgtgggtcagtttcctgtctttttaatttagttcagttcctggctgcagCTCAACATCGCCAACCCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTMapped 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|211199269|gb|FL277456.1|FL277456EST: GCTCGAGCTCCTCGCGTCCTGCGARCGCGCGCCGCAACGCCACCATGAAG TTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCGTCCTGCGAGCGCGCGCCGCAACGCCACCATGAAGgtaagctact ... cactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT
EST:
gi|211199270|gb|FL277457.1|FL277457EST: GCTCGAGCTCCTCGCGTCCTGCGAGCGCGCTCCGCAACGTCACCATGAAG TTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCGTCCTGCGAGCGCGCGCCGCAACGCCACCATGAAGgtaagctact ... cactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
atctgat putative branch site (score: 4)
cactttcc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctactcccggcctttcccgcgataggcggtgtttgtgggaatctagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC