Sequence
atgc intronic sequence ATGC exonic sequencegtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctttccgcttattattaaattgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
Basic information
species | Glycine max |
transcript | GLYMA07G26540.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 3
gtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctt--tccgcttattattaaattgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
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------------------------gtaagtgaaatatatcttttcttctagttttaagctgctac----cgagttgctcgtggtagat---ttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctt---tttttgcagGGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G14840.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctttccgcttattattaaattgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
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-----------------------------------gtcattgctgatacatattaatatttaaatt-ctcttgctgctt-caaattgtgattcatattca----cggagattaacttatactattgcc-accaccg--ttatgtttggacagGGAGAAATGCAACAACTACGCGACAAACTTGCCATAGCTGACCGAGCTGCAAAATCTGAAGCTCAGCTGAAG
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttctt-gacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctttccgcttattattaaattgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
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---------------------------gtttactttgatatgatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatct-acattc----tcacttcttgatcctca-------acttttttgcagGGAGAAATGCAGCAACTTCGTGATAAGCTCGCCATAACAGACCGGGCTGCAAAATCCGAGGCACAGTTAAAA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttccca--catttggcttcgctt-tccgcttattattaa-attgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
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gtgatgcctgtaaggcagtggcttgaagaacgta-gatttttgcaggtca-ttgctgatacatattaatattta-aattctcttgctgcttcaaattgtgattcatattcacggagattaacttatactattgccaccaccgttatgtttggacagGGAGAAATGCAACAACTACGCGACAAACTTGCCATAGCTGACCGAGCTGCAAAATCTGAAGCTCAGCTGAAG
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttctttt---atattaatttcccacatttggcttcgctttccgcttattattaaattgcattctt-atagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
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--------------------------------gttacttttgatattttatttttgggcttctgttactgcttcgagttgtgattcatattcacaggaaccattgtaacttgagtaagtgcattctttaaccattttcctgtttctttttggacagGGAGAAATGCAACAACTACGTGACAAACTTGCCATAGCTGATCGAGCTGCAAAATCTGAAGCTCAGCTAAAGMapped 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|193665776|gb|FK609663.1|FK609663EST: ATAAAGTGATGCCTGTCAAACAGTGGCTTGAAGAACGTCGATTCTTGCAG GGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCA
genomic: ATAAAGTGATGCCTGTCAAACAGTGGCTTGAAGAACGTCGATTCTTGCAGgtaatatttt ... attcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttcccacatttggcttcgctttccgcttattattaaattgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
tattaat putative branch site (score: 2)
cattctt putative PPT
ttattattaaattgca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctttccgcttattattaaattgcattcttatagGGAGAAATGCAGCAACTTCGTGACAAGCTTGCTATAGTTGAGCGCGCTGCAAAGTCTGAAGCACAATTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC