Sequence
atgc intronic sequence ATGC exonic sequencegtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA
Basic information
species | Glycine max |
transcript | GLYMA11G01940.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01940.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA
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-------------aattacagcactgtttagaactcaaata-----gtgttgg--atgctcagaactgtcactttgttttgatgtta-------aatcttttttctaaaatttatttctacttgcagGATGTCAAGCATACAACCTTGGAACAGGAAAGGGAACATCAGTGTTGGAAATAGTTAATGCATTTGAGAAAGTTTCTGGAAAG-----------------
upper sequence: GLYMA11G01940.4 (Glycine max), 3'ss of exon 6
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA
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-----------gtatgcttttcttcttct-tttcataagtac-------ctcattgtctc---gacaat-acatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG-----------------
upper sequence: GLYMA11G01940.4 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggt-gaatttatagtggtaaaatttt---attttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA
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-----------------------------agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatga--acagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG-----------------
upper sequence: GLYMA11G01940.4 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA
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------------------ctcgagcaaatggaagtaaaacttgtcgacattgattttcatt-------tgatacctaactg--ctaaaacttgtaaacattgattttcatttgatatctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG-----------------Mapped 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|16105481|gb|BI893221.1|BI893221EST: AGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAGgtatcattct ... gtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST:
gi|19346921|gb|BM891809.1|BM891809EST: AGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTTGGAG
genomic: AGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAGgtatcattct ... gtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTT-GGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA
ttttaat putative branch site (score: 3)
tgaatttatagtggta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG