Sequence
atgc intronic sequence ATGC exonic sequencetgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA
Basic information
species | Glycine max |
transcript | GLYMA17G37820.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 3
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattt-tcatccaaactccaacgatgtgttattg--ttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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--------------------------------------------------attcctatgaa-attcccgg---gaaaagcctccaatccaaatgagcccttaaggttattagtagatgctaggaatttaatgtgtgctttttttttatgtgtagGCTTTGGACAAGATTAGGTTCCTGGCTCTCACTGATAAGGAGGTTTTGGGCGAAGGTGACACTGCTAAGCTTGAAATCCAG
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G110574_T01 (Zea mays), 3'ss of exon 7
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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----------------------------------------------------------------gtatgtattacatactgaccc---tagtgtttgttctacattgtg--gatgc-tcgaaattaactaggtgttctgcatgt-ctgtagGCGTTGGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTTTGGGTGAAGGGGACACTGCAAAGCTTGAGATTCAG
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G063988_T02 (Zea mays), 3'ss of exon 10
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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----------------------------------------------------------------gtatgtattacatactgacccctgtg---tttgttctacattgtg--gatgc-tcgaaattaactgggtgttctgcatgt-ctgtagGCGTTGGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTTTGGGTGAAAGGGACACTGCAAAGCTTGAGATTCAG
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G141931_T01 (Zea mays), 3'ss of exon 3
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgt-ttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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----------------------------------------------------------gtatgtattacatct----gacccctgtgtttgt-tctgcattgtg--------gatgc-tcgaaattaactgggtgttctgcatgt-ctgtagGCGTTGGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGGGACACTGCAAAGCTTGAGATTCAG
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 3
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactcca-acgatgtgttattgttaatgacaaatgatgct-tgcat---tctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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---------------------------------------------------------------------------gtatgtattgcttctgacccctgtgtttattctgcattgtggatggtcgaaattaactg-tggtgttctgcatgtctgtagGCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G022909_T01 (Zea mays), 3'ss of exon 4
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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----------------------------------------------------------------gtatgtactacatactgacccctgtg---tttgttctgcattgtg--gatgc-tcgaaattaactgggtgttctacatgt-ctgtagGCT--GGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGGGACACTGCAAAGCTTGAGATTCAG
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 3
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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----------------------------------gtaagcagcttcgtgta--cattgttttagtgagtttttgggatacctcg---ttaaat----aggggaact--aataa-gtgtctgtgttggtgat--------------tttcagGCCTTGGACAAAATTAGGTTCCTTGCACTCACTGACAAAGACGTTTTGGGTGAAGGTGACACTGCTAAGCTTGAGATCCAG
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-
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-----------------------------------------------------------------------gtaagtattattttgtttgtttctaggaactttctttctgaagttgttact--taatggtaattc-tgcttg-atttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGMapped 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|298170585|gb|HO019209.1|HO019209EST: TACAGTAACAAGGATATCTTCCTCAGAGAGTTGATTTCCAATGCTTCTGA TGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGG
genomic: TACAGTAACAAGGATATCTTCCTCAGAGAGTTGATTTCCAATGCTTCTGAtgtaagcgtt ... ttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA
tgttaat putative branch site (score: 3)
ttattgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT