Sequence
atgc intronic sequence ATGC exonic sequencegtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
Basic information
species | Glycine max |
transcript | GLYMA13G39990.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 7
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
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-------------------------------------------------------------------------------------------------gtacactctgctc-ctttgatatcctttataat--tgtctaaattggaagg------tgattctaaa-gatactgttttgtttaa-attgt--agGTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAG
upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 7
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
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------------------------------------------------------------------------------------gtctgctactttg-----ctctgatgctattgtcattctctcaggtgctcaattttgaaggatat-------cttctaaa-gatttatttatgcacata--catgtagGTGGTATGCCAAAAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATCTGGGATGAGGACCTTGGGGTGGAGCATTTCAATGCGGAG
upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtga-tcacattta-actttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
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------------------------------------------------------------------------------gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatct-agtgcta-atttttttgtttgtgcacacaactct-----------------agGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
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-------------------------------------------------------------------------------------------------------gttagtcatctggtcat--ttaccggttattaagta--tgtttgtcgagtatgtttttat-cgaaattctc-tact-ggttttg-gcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaatt-cttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
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------------------------------------------------------------------------------gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgttt-----------atctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
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--------------------------------------------------------------------------------------ggagagacacggcattattggctaagctgaaactttttc----tgctg--cagatagttaatactttttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAGMapped 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|33390489|gb|CA853684.1|CA853684EST: GAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAAGGAAACAAACTAAATG GTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATA
genomic: GAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAAGGAAACAAACTAAATGgtatagtttt ... tgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATA
EST:
gi|13181457|gb|BG352797.1|BG352797EST: GAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAAGGAAACAAACTAAATG GTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATA
genomic: GAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAAGGAAACAAACTAAATGgtatagtttt ... tgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATA
EST:
gi|18848780|gb|BM567892.1|BM567892EST: GCAAGGAAACAAACTAAATG GTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATA
genomic: GCAAGGAAACAAACTAAATGgtatagtttt ... tgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
ttttatacaattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG