Sequence
atgc intronic sequence ATGC exonic sequencegtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgagcggcgagccgcccatgttgagctcgtggctgatctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G801409_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 1
gtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacct-------cgactcgccttgctc--------gccggcggcggccttttc-ttcgccgagcggcgagccgcccatgttgagctcgtggctgatctgatggg--------cttgttgtgatctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG-
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--gtaaccatctcatccttcgcctcccctcgattcgctgctcgcctgcggcggcggcgcggctaggccatttcgttgccggcgtcggcctgcgggttcaccggtgggtgctttgccgcgtttgcttttgtcgtggatctgatggagtttgcgttttctcgcgggattttgtagGTAAGGGAGGAGGAGTAAG-AAGATGTCGCACAGGAAGTTCGAGCACCCGAGGCACGGATCCCTCGGCTTCCTCCCGAGGAAGCGCTCCTCCCGCCACCGC
upper sequence: GRMZM5G801409_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
gtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgagcggcgagccgcccatgttgagctcgtggctgatctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGA----GGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG-----
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--gtatgttcccaa-ccatttcctgcgt--tctgttctgctctgttcggttatgatagatc-----cgttagtgttttctcttccg-------------ttttgcttttcttatgaatgaatgaatg--catgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
upper sequence: GRMZM5G801409_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G30810.1 (Glycine max), 3'ss of exon 1
gtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgagcggcgagccgcccatgttgagctcgtggctgatctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG--------
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------------------------------------------------gatagtagt-cacaatattaacgacgatttgtttcctcatttttgtg------gtgttaaatttatcacctgccactagtcttcattacttatttttgtttttaaagGAGGAGAATA----AGGATGTCTCACAGGAAGTTCGAGCACCCAAGGCACGGGTCACTGGGATTTCTCCCCAGGAAGCGTGCTGCTCGTCACAGGGGAAAAG
upper sequence: GRMZM5G801409_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G36780.1 (Glycine max), 3'ss of exon 1
gtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgagcggcgagccgcccatgttgagctcgtggctgat-ctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG--------
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----------------------------------------------------atattaa-caacgatttctttcctcattttgtcgtgtta-aaatttatcacctgtctctcgttttcattactgacg--tttatttttattttttgtttttgaagGAGGAGA-------AGGATGTCTCACAGGAAGTTCGAGCACCCAAGGCACGGTTCACTGGGATTTCTTCCCAGGAAGCGTGCTGCTCGTCACAGGGGAAAAG
upper sequence: GRMZM5G801409_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G00280.1 (Glycine max), 3'ss of exon 1
gtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgagcggcgagccgcccatgttgagctcgtggctgatctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG-------
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------------------------gtatgttttcaaccatttcctgcgatctgttctgttcgtttacgatagatctgtt-------agtgttttatcttccgttttgttttt--------tcttatgaatgaagtcttatatttgacagTTGAATTTGGAAA-------AAGATGTCTCACCGGAAGTTCGAGCACCCGAGACATGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAAAGMapped 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|211350898|gb|FL394316.1|FL394316EST: ACTGCCGCGCCGCCACCCTCTACAG ATAAGGAAGAGGAGGAGGGCAGGATGTCGCA
genomic: ACTGCCGCGCCGCCACCCTCTACAGgtgaatgtaa ... tctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCA
EST:
gi|211290641|gb|FL414835.1|FL414835EST: ACTGCCGCGCCGCCACCCTCTACAG ATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCA
genomic: ACTGCCGCGCCGCCACCCTCTACAGgtgaatgtaa ... tctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccgcccatgttgagctcgtggctgatctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG
atctgat putative branch site (score: 4)
tctcctgc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgagcggcgagccgcccatgttgagctcgtggctgatctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG
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