Sequence
atgc intronic sequence ATGC exonic sequence...aaaaagaataagttgacagacagtggtttcattggtagaggtccaccatcattatcttcctaaaggccaaaactaatctgttttatctttttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA
Basic information
species | Glycine max |
transcript | GLYMA20G37330.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
------------------------------aaaaagaataagttgacagacagtggtttcatt-ggtagaggtccaccatcattatcttcctaaaggccaaaactaatctgttttatctttttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA
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gtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgcca--tatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 6
-------aaaaagaataagttgacagacagtggtttcattggtagaggtccaccatcattatcttcctaaaggccaaa-actaatctgtttt-----------atctttttgctga-aagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA
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gtaggtgaacttttatctgtttctatcttggagttttcctaaataaactattcaattttcatatttactcagttcaattgttgatttattgtttgatatacggatatactttttgacaagGTTCGAATTATGCGTCGGCTGCGCCATCCAAATATTGTTCTCTTTATGGGTGCTGTTACACGCCCTCCGAACTTATCTATTGTATCTGAATATCTTCCAA
upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 6
-------aaaaagaataagttgacagacagtggtttcattggtagaggtccaccatcattatcttcctaaaggccaaa----actaatctgttttatct----------ttttgctga-aagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA
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gtaggtgaacttttatctgtttctatcttggagttttcgtaaataaataattcaattatcatatttactcagtccagttgttgctttattgtttgatatacggatgtactttatctgacaagGTCCGAATTATGCGTCGGCTGCGCCATCCAAATATTGTTCTCTTTATGGGTGCTGTTACACGCCCTCCGAACTTATCTATTGTATCTGAATACCTTCCAA
upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
-aaaaagaata--agttgacagacagtggtttcattggtagaggtccaccatcattatcttcctaaaggccaaaactaatctgttttatctttttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA
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aaaatattatattatttctatgttggagacttggctggtaattttgttataaagcaaaaatgttaa--cttgatgtctgtcttttttgt-tctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAAMapped 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|6566093|gb|AW233853.1|AW233853EST: TTTTGGATCAGGATTTTTCAGGTGCTGCATTGTCAGAATTCAAAAGAGAA GTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTT-ATGGGT
genomic: TTTTGGATCAGGATTTTTCAGGTGCTGCATTGTCAGAATTCAAAAGAGAAgtaagtacta ... ttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGT
EST:
gi|9564976|gb|BE474476.1|BE474476EST: TTTTGGATCAGGATTTTTCAGGTGCTGCATTGTCAGAATTCAAAAGAGAA GTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGT
genomic: TTTTGGATCAGGATTTTTCAGGTGCTGCATTGTCAGAATTCAAAAGAGAAgtaagtacta ... ttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatcattatcttcctaaaggccaaaactaatctgttttatctttttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA
aactaat putative branch site (score: 2)
tctgttttatcttttt CT-rich tract
tgttttatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaagaataagttgacagacagtggtttcattggtagaggtccaccatcattatcttcctaaaggccaaaactaatctgttttatctttttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT