Sequence
atgc intronic sequence ATGC exonic sequenceTGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAGAAGgttattcatgttacctaactaaagtcttcatgtctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag
Basic information
species | Glycine max |
transcript | GLYMA13G40580.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g02670.2 (Oryza sativa), 5'ss of exon 5
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAGAAGgttattcatgttacctaactaaagt-cttcatgtctcattgctttgtattga-aattttgaaatctatttcttactttgctacttgattctgcag-------
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------TGAGGTCCTTGAGGGCTATAATTGCACAATTTTTGCTTATGGGCAAACTGGTACTGGGAAAACCTACACAATGGAGGGAGGTGGAACTAGAAAGACCA---AGgtaa---aaaaaaagtgcttgagatcatttaaaatcgcatttttggtttttctgcatgttctttacaat-tgacttgtgcttgtaacatccag
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G45850.1 (Arabidopsis thaliana), 5'ss of exon 4
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAGAAGgttattcatgtta-------cctaactaaagtcttcatgtctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag
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TGTGTTTGAAGTACTTGAGGGTTACAACTGTACCATATTTGCGTATGGTCAGACCGGAACTGGAAAGACGTATACGATGGAAGGAGGTGCAAGGAAAAAGgttggctcctctaaaacgaacctaacatgattctgtatgattcagatgtatttgtcatggtttttaa-taaatagctacggttgctatttgtag------
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G28620.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAGAAGgttattcatgttacctaa-ctaaagtcttcatgtctcattgctttg-tattgaaattttgaaatctatttctt--actttgctacttgattctgcag
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TGTCTTTGAGGTTCTTGATGGGTATAACTGCACCATCTTTGCATATGGGCAAACAGGAACTGGTAAGACATACACAATGGAAGGAGGAGCAAGAAAAAAGgt-----acgctaactattccaagaacatcatttgaagtttctttactgatggtaactgaatcctcatttgatggaacatatttcttttgttgccag
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 5'ss of exon 4
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAGAAGgtt--attcatgttacctaactaaagtcttcatg-tctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag
|| ||||||| |||||||||||||| ||||| || ||||| ||||| ||||| |||||||| || ||||| |||||||||||||| ||||| || |||||| ||| |||| || | || | | | | | | ||||| |||| ||| | || |||| | |||| | | |
AGTAAATGAAGTTCTTGAGGGCTATAATTGCACAATATTTGCCTATGGTCAGACAGGGACAGGCAAAACATATACAATGGAAGGAGGCGCAAGGAAAAAGgtttaattttcattacatatatcaactatgtgtacttttaatgcttcccattgg---tttaatttccatttgatgcttt--ttgtag---------
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S158_7V6.1 (Physcomitrella patens), 5'ss of exon 3
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAGA--AGgttattcatgttacctaact---aaagtcttcatgtctcattgctttgt-attgaaattttgaaatctatttct--tactttgct---------acttgattctgcag----------------------------------------------------------
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---GAACGAGGTCCTGGACGGTTTTAACTGCACGATATTTGCCTATGGCCAGACTGGGACAGGGAAAACCTACACCATGGAAGGATCGGGAAGAAAATCCAAGgtattgggttgtcctggtttgcgaagtcttttgaacttgctgcgctaccgtctacctcatccgcttgatttcgagtgtcttgcggaaaggccaacttgattgatgagcttatgttgaattgaagtgggaaatatatacttgtctaagacgaataatgtcttacag
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S315_14V6.1 (Physcomitrella patens), 5'ss of exon 3
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAG---AAGgttattcatgttacctaact--aaagtcttc--atgtctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag-----------------------------------------------------------------------
| || | | || || | ||||||||||| ||||| ||||||||||| ||||||||||| || ||||| ||||||||| || ||||||| ||||||| || || | |||||| | || | || || | || |||| ||| || | | | ||| || | | | ||||
---CAACGAGGCCTTAGATGGTTTCAACTGCACTATATTTGCTTATGGACAGACTGGGACAGGGAAAACCTACACCATGGAAGGATTAGGAAGAAAGTCGAAGgttaagtatcttccagggtgggaaagtcgttgaatttttctctgggtcacatagaaactttcgcatgtgtctacctctt-gccaggaggcta-gcagtatcaaagaacattggaatggatcaaagttgggatccgattgttgtctaatactgaaaaattacattgcag
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S6_143V6.1 (Physcomitrella patens), 5'ss of exon 3
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGG---AGGAGCAAGAAAGAAGgttattcatgttacctaacta-aagtcttcatgtctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag----------------------------------
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---CAACGAGGTTTTGGATGGCTACAACTGCACTATTTTTGCATATGGGCAGACCGGGACCGGAAAGACCTTCACTATGGAAGGGTCAGGAATGAAGTCGAAGgtagtaagcctcacgtacccctgaacgtttatatgttgctcagtttcataaaggcgttgtcactcagctaatttactggtcgttgaatggtcgaaacataggaatcatcatttacaatttctttgcag
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ12240 (Selaginella moellendorffii), 5'ss of exon 3
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAG---AAGgt-----tattcatg--ttacctaactaaagtcttcatgtctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag
| | ||||| || || |||| ||||| || ||||||||||||||||||||||| || ||||| || ||||| ||||| |||| || |||||| ||||| ||| ||| || | || ||| | | | | |||||| | || | |
---GAACGAAGTTCTCGAAGGCTTCAACTGTACCATTTTTGCGTATGGACAGACCGGAACGGGGAAAACTTACACTATGGAGGGAGCAGGAAGAAAACCCAAGgtatgaatatcgatgcctttcttatctagaatgtcta--tctcatctttatggttccag-----------------------------------------
upper sequence: GLYMA13G40580.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ25853 (Selaginella moellendorffii), 5'ss of exon 3
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAG---AAGgt-----tattcatg--ttacctaactaaagtcttcatgtctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag
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---GAACGAAGTTCTCGAAGGCTTCAACTGTACCATTTTTGCGTATGGACAGACCGGAACGGGGAAAACTTACACTATGGAGGGAGCAGGAAGAAAACCCAAGgtatgaatatcgatgcctttcttatctagaatgtcc-tatctcatctttatggttccag-----------------------------------------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|207726675|gb|GD701549.1|GD701549EST: ATACACAATGGAAGGAGGAGCAAGAAAGAAG AATGGCGAATTTCCGAGTGATGCTGGTGTCATCCCAAGAGCTGTGAAACAG
genomic: ATACACAATGGAAGGAGGAGCAAGAAAGAAGgttattcatg ... gattctgcagAATGGCGAATTTCCGAGTGATGCTGGTGTCATCCCAAGAGCTGTGAAACAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGTGTATGAAGTGCTTGAGGGCTATAACTGCACTATTTTTGCGTATGGACAGACCGGGACAGGGAAGACATACACAATGGAAGGAGGAGCAAGAAAGAAGgttattcatgttacctaactaaagtcttcatgtctcattgctttgtattgaaattttgaaatctatttcttactttgctacttgattctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG