Sequence
atgc intronic sequence ATGC exonic sequencegtacttttattgagtctagcacgagaatatgtctgcactaacttgaccataaaatatttctcttatttttcatccaatatttgttggaatttgatatttggtaagttactttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAGGATCTGCTAAAGAATATCAGAACTCAAGTCTTGCTGAAGCTCATCAAAC
Basic information
species | Glycine max |
transcript | GLYMA03G00670.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 9
gtacttttattgagtctagcacgagaatatgtctgcactaacttgaccataaaatatttctcttatttttcatccaatatttgttggaatttgatatttggtaagttactttc-cagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAGGATCTGCTAAAGAATATCAGAACTCAAGTCTTGCTGAAGCTCATCAAAC
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------------------------------gtcagcgtctatttcttcagaaattttatctcttaattttc------catgtact--aatgcaagtgttatcaacttctttttgcagAGTAATAGAAGAACAATAATGGATGATCCTTTTATCCGTAACTATATTGAGGATCTGTTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAAC
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 9
gtacttttattgagtctagcacgagaatatgtctgcactaacttgaccataaaatatttctcttatttttcatccaatatttgttggaatttgatatttggtaagt--tactttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAGGATCTGCTAAAGAATATCAGAACTCAAGTCTTGCTGAAGCTCATCAAAC
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gtaagcg-attgtgtgcaccatgattttatgtaatgattaattttat-attgtcctcttcttccatcatcactagcttttctcatggaagtatatgttggaaaaatggtgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAGGATCTGTTAAAAAATATTAGAACACAAGTGTTGCTCAAGCTCATCAAAC
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------gtacttt-tattgagtctagcacgagaatatgtc-tgcactaacttgaccataaaat-atttctcttatttttcatccaatatttgttggaatttgatatttggtaagttact---ttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAGGATCTGCTAAAGAATATCAGAACTCAAGTCTTGCTGAAGCTCATCAAAC
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gtacattcttctagattggatttgagacatgttcttggggattgtagttatgttcgcgttccctatggtgtaaggtatctgacgtaaaattgtgagattctttgtggggatcatatgatcatgcgttatatgcatggtacttagtctgctg---tttcgttttggtgatgtttttggcttatagAGTAACAGAAAGACCATAATGGATGACCCTTTCATTCGGAACTACATTGAAGATCTGCTCAGTAAAATCCGCACGCAAGTGTTGCTGAAGCTCATTAAACMapped 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|11273882|gb|BF324271.1|BF324271EST: GGAATTTGAGAAAATCTTGAAG AGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAG
genomic: GGAATTTGAGAAAATCTTGAAGgtacttttat ... tactttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAG
EST:
gi|58014800|gb|CX701542.1|CX701542EST: TAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG AGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAG
genomic: TAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAGgtacttttat ... tactttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatttttcatccaatatttgttggaatttgatatttggtaagttactttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAGGATCTGCTAAAGAATATCAGAACTCAAGTCTTGCTGAAGCTCATCAAAC
atttgat putative branch site (score: 5)
ttactttcc putative PPT
aatttgatattt 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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gtacttttattgagtctagcacgagaatatgtctgcactaacttgaccataaaatatttctcttatttttcatccaatatttgttggaatttgatatttggtaagttactttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAGGATCTGCTAAAGAATATCAGAACTCAAGTCTTGCTGAAGCTCATCAAAC
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