Sequence
atgc intronic sequence ATGC exonic sequencegtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgttgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG
Basic information
species | Glycine max |
transcript | GLYMA05G09460.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgttgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG
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gtatgtatg-atgcccaccaccatcctctctctattct----tttctttgc-ctccaccaattaattgtagcttaaaattttgacaagaaatcatgccatgtgtggtagtt---aaaattctgt--ggt-taccttttttttttt--ttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgt-tgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG-------
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----------------------------------------------------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccac-tctggttt-----taattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgt-tgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG
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----------------------------------------------------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccac-tctggttt-----taattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 4
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgttgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattat-gtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG
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-------------------------------------------gtatttgagcttttctt---ttttctgaaaaaaaaaatcttgaaa--atttgtattcct-ttattctactaattccaattatataatttatctgacttttct--atat-tcttttgatgaagCAAATATGTCACCGGGACTTGAAGTTGGAAAATACTTTGTTGGATGGAAGCCCAGCTCCACGTTTGAAGATATGTGATTTTGGGTACTCCAAGMapped 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|7640623|gb|AW734850.1|AW734850EST: GATTCTTCTTTCAGCAACTCATATCCGGGGGCAGCTATTGCCATGCTATG CAAGTATGTCAT
genomic: GATTCTTCTTTCAGCAACTCATATCCGGGGTCAGCTATTGCCATGCTATGgtaattgaac ... cttcacgaagCAAGTATGTCAT
EST:
gi|7685757|gb|AW756405.1|AW756405EST: GATTCTTCTTTCAGCAACTCATATCCGGGGTCAGCTATTGCCATGCTATG CAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTNTGCTGGATGGAAGC
genomic: GATTCTTCTTTCAGCAACTCATATCCGGGGTCAGCTATTGCCATGCTATGgtaattgaac ... cttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGC
EST:
gi|120495545|gb|EH223712.1|EH223712EST: GATTCTTCTTTCAGCAACTCATATCCGGGGTCAGCTATTGCCATGCTATG CAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGC
genomic: GATTCTTCTTTCAGCAACTCATATCCGGGGTCAGCTATTGCCATGCTATGgtaattgaac ... cttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG
gtctgat putative branch site (score: 4)
tgtctcttc putative PPT
tcttcttataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgttgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG