Sequence
atgc intronic sequence ATGC exonic sequencegtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA11G01940.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG
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-------------aattacagcactgtttagaactcaaata-----gtgttgg--atgctcagaactgtcactttgttttgatgtta-------aatcttttttctaaaatttatttctacttgcagGATGTCAAGCATACAACCTTGGAACAGGAAAGGGAACATCAGTGTTGGAAATAGTTAATGCATTTGAGAAAGTTTCTGGAAAG
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 6
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG
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-----------gtatgcttttcttcttctttt-cataagtac-------ctcattgtctc---gacaat-acatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggt-gaatttatagtggtaaaatttt---attttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG
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-----------------------------agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatgaa--cagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 6
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG
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------------------ctcgagcaaatggaagtaaaacttgtcgacattgattttcatt-------tgatacctaactg--ctaaaacttgtaaacattgattttcatttgatatctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAGMapped 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|9902956|gb|BE611924.1|BE611924EST: AGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG GTTGTGAGGTTTATAACCTGNGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAGgtatcattct ... gtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG