Sequence
atgc intronic sequence ATGC exonic sequencegtctaacaaagcaaacttttgatgaaactatatttaaataaaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
Basic information
species | Glycine max |
transcript | GLYMA11G34120.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
gtctaacaaagc-aaacttttgatgaaactatatttaaata-----aaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
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gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgac-atattggaatattga-agGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g38370.3 (Oryza sativa), 3'ss of exon 3
gtctaacaaagc-aaacttttgatgaaactatatttaaata-----aaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA--------------------
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gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgac-atattggaatattga-agGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAGTCTGTTGCTATTTCTCCTA
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 3'ss of exon 5
gtctaacaaagcaaacttttgatgaaactatatttaaataaaggttttca-attttttctcatgcttat----ctgctaattttgcca-----gGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
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--gtaaatggatgaactgttcgctagttcat-tatgatcaatagcccaaacagttcttttgctgataatactgttgttaaattggacacctgagGTTGGAGAGGTTGCAAAGATCACATGCAAGCCAGAATATGCTTATGGAGCTGCAGGTTCACCTCCAGAGATACCGCCAGA
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 2
gtctaacaaagcaaacttttgatgaaactatatttaaataaaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
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gtatgtcaacgtttgcgtctctcgctttggcctttcaccatctctgtgtgacatggtctg--gcatatccaaaaaaatta--agGTTGGCGAGGTTGCAAAAATTACATGCAAATCAGAATATGCATATGGAGCTGCAGGCTCACCACCAGAGATACCTCCTAA
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G55520.1 (Arabidopsis thaliana), 3'ss of exon 3
-gtctaacaaagcaaacttttgatgaaactatatttaaataaaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
| |||| | | || | | | | | | || | || | || | | || || || | |||| ||||||||||||||||||||||| || || |||||||||||||| || || || || || |||||||| || || || || ||
gtttctacaattttgagtctttcttctatccttataatctgaacgcttcagttattatatacaactgatttgattttttttacagGTTGGAGAAGTTGCAAAAATTACATGTAAGCCAGAATATGCTTACGGAAGAGCCGGGTCTCCTCCCGACATCCCACCTGA
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
----gtctaacaaagcaaacttttgatgaaac-tatatttaaataaaggttttcaattttttct-catg--cttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
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gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAMapped 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|208087121|gb|GD887169.1|GD887169EST: GAAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCTGTGAAAACCATGAAG GTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCNGT
genomic: GAAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCTGTGAAAACCATGAAGgtctaacaaa ... attttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGT
EST:
gi|208202125|gb|GD998728.1|GD998728EST: TGGGAAATTGCTGTGAAAACCATGAAG GTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGT
genomic: TGGGAAATTGCTGTGAAAACCATGAAGgtctaacaaa ... attttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttaaataaaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
tgctaat putative branch site (score: 2)
ttttgcc CT-rich tract
taaataaaggttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaacaaagcaaacttttgatgaaactatatttaaataaaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC