Sequence
atgc intronic sequence ATGC exonic sequence...cctttgtcttaacctgaattggtagagttgcagttgcaatattctattcccccaccacacaaaaaaagtctacaaacatgtatctttttttttccctcagGTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTGATCAAACAAAACCGAAAAGTGATAATGCCCATCATCTTCCCTGCATTGG
Basic information
species | Glycine max |
transcript | GLYMA18G01400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G01400.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g62730.3 (Oryza sativa), 3'ss of exon 3
----cctttgtcttaacctgaattggtagagttgcagttgcaatattctattcccccaccacacaaaaaaagtctacaaacatgtatctttttttttccctcagGTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTGATCAAACAAAACCGAAAAGTGATAATGCCCATCATCTTCCCTGCATTGG
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tgcggggaattgttaatgcaaatta-tattgaagcagcagaaacatgatatacgcatattggttgatggattttatctaata---gtgcttatgctacttctagGTTGCTGAGAGAGCATTGTTTTTGTGGAACAATGATCATATCGAGAATCTGATCAAACAAAATAGTAGGGTGATCTTACCTATCATCTTCCCTGCACTCG
upper sequence: GLYMA18G01400.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0010g02350.t01 (Vitis vinifera), 3'ss of exon 1
--cctttgtcttaacctgaattggtagagttgcagttgcaatattctattccccc--accacacaaaaaaagtctacaaacatgtatctttttttttccctcagGTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTGATCAAACAAAACCGAAAAGTGATAATGCCCATCATCTTCCCTGCATTGG
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gggtatttccttgaagctacttgttctgaaaatagccaccatgcaatgttgtctttaatttctgaatcacactccttgaaactgatgcttgttttttc----agGTGGCAGAGAGAGCTTTGTTCCTATGGAATAATGGTCACATTGAGAACTTAATCAAACAAAATCGCGGTATTATATTGCCCATCATCTTCCCTGCCTTGGMapped 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|192295090|gb|FG986809.1|FG986809EST: TGCCATTATTTCGTCGCATTGCACGTTGTTTGAATAGCCCTCATTTTCAG GTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTG
genomic: TGCCATTATTTCGTCGCATTGCACGTTGTTTGAATAGCCCTCATTTTCAGgtatgaattc ... tttccctcagGTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTG
EST:
gi|254339952|gb|GR858077.1|GR858077EST: TGCCATTATTTCGTCGCATTGCACGTTGTTTGAATAGCCCTCATTTTCAG GTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTG
genomic: TGCCATTATTTCGTCGCATTGCACGTTGTTTGAATAGCCCTCATTTTCAGgtatgaattc ... tttccctcagGTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcccccaccacacaaaaaaagtctacaaacatgtatctttttttttccctcagGTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTGATCAAACAAAACCGAAAAGTGATAATGCCCATCATCTTCCCTGCATTGG
catgtatctttttttt CT-rich tract
atgtatcttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctttgtcttaacctgaattggtagagttgcagttgcaatattctattcccccaccacacaaaaaaagtctacaaacatgtatctttttttttccctcagGTGGCAGAAAGAGCCTTGTTCTTGTGGAACAATGATCACATCATGAACTTGATCAAACAAAACCGAAAAGTGATAATGCCCATCATCTTCCCTGCATTGG
- - - - - -acctgaa
- - - - - - - - - - - - - - - cagttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacat