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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccctttcttcgcactctcacttttagggtttccaattttatttttttatgaattcggtgcgtctgatttgggtttattcttttttaatatctcg...

Basic information

species Glycine max
transcript GLYMA15G11350.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 1
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccctttct---tcgcactctcacttttagggtttcca--attttatttttttatgaattcggtgc--gtctgatt---tgggtttattcttttttaatatctcg---------
 ||||| || ||||| || || |||||   |||||||||  ||||||||||||| || |||||||| || || ||||||||| |||| ||  |||| || ||    | || |||   || | |||   |        ||| ||  ||| || | | |  |  ||  |||||  || ||| |   || | | ||    |  |    ||            
GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctctctctctctctctctccgcccgcccctctttacatgattctactctctcctcgatctggtgcttgtttgagtgcctgcgctgatggcctaatgccctccttgcctcgcag

upper sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgta----atcccctttcttcgcactctcacttttagggtttccaattttatttttttatgaattcggtgcgtc--tgatttgggtttattcttttttaatatctcg-----------------------------------------------------------
 ||||| || ||||| || || |||||   |||||||||  ||||||||||||| || |||||||| ||||| ||||||||| |||| ||  |||| || |||     || || | | || | ||||| || |     | ||    | | | | | | |   |      |  |  ||| | ||   |  |  | |||     ||                                                             
GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag

upper sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G082976_T01 (Zea mays), 5'ss of exon 1
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccctttcttcgcactctcacttttagggtttccaattttatttttttatgaattcggtgcgtctgatttgggtttattcttttttaatatctcg-------------------
 ||||| || ||||| || ||||||||   |||||||||  ||||||||||||| || |||||||| || || ||||||||| |||| ||  |||| || |||  |  ||| |  | |  || ||   | |||   | |   ||   |     |||    | |    ||| || |     | || ||| |       | |                   
GATGGCGCAGGCGGTGGAGGAATGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgta-ccggcttccccctccttcccatgatcaggagattc---ttctctcgcccatgtcgccaggatctctaatctcatccttttttttgtgcgcccgttggctggccccggctgtgcag

upper sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 1
lower sequence: AT4G21810.1 (Arabidopsis thaliana), 5'ss of exon 1
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccctttctt-cgcactctcacttttagggtttc-caattttatttttttatgaattcggtgcgtctgatttgggtttattcttttttaatatctcg-
 ||||||||||| || ||||| ||||| |||||||||||  | || || || || |||||||| || ||||| ||||||||| |||| ||||| || || ||       | |||  | ||      | |||||  || | |   || || |  |||    |||  ||      | |||  | | |   ||| |  ||| |   
TATGGCTCAAGCCGTAGAAGAGTGGTACAAGCAGATGCCGATTATAACCCGGTCGTATCTCACGGCGGCTGTAGTCACCACCGTCGGGTGTTCGCTCGAGgtttgaagttctctgactcatgaaagcctttagctttgctctgattgatctgattagtttttccttgaa---aaattgaatctttgtgtttctgttatgtatg

upper sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 1
lower sequence: AT4G04860.1 (Arabidopsis thaliana), 5'ss of exon 1
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccctttcttcgcactctca----cttttagggtttccaattttatttttttatgaattcggtgcgtctgatttgggtttattcttttttaatatctcg
 |||||||| || || |||||||||||||| ||||||||  | ||||| |||||||||||||| || |||||| |||||||| ||||||||||||| ||||||    | |   | |  | || |      |||| ||| |||    | |    || | | |||| || |  ||  |||  | ||  || | ||||         
TATGGCTCAGGCTGTAGAAGAATGGTATAAACAGATGCCGATTATCACTCGCTCTTATCTCACGGCGGCTGTTATCACCACCGTCGGATGTTCCCTCGATgtacgtgcttgcttgcttattcgcgaatcttttttggggttc----tctgaaattctctaaattagg-gtttcatattctgattgtttttgttttgcag-----

upper sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 1
lower sequence: Vv00s0704g00010.t01 (Vitis vinifera), 5'ss of exon 1
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct---ttcttc--gcactctcacttttagggtttccaattttatttttttatgaattcggtgc-gtctgatttgggtttattcttttttaatatctcg
|||||||||||| |||||||||||||| |||||||||||  ||||||| ||||||||||||||||| ||  | |||||||||||||| || || || || |||  || ||   |  |||  ||  | ||  | |   ||| | || | || || |||  |   ||  |||  |  |   | ||||||  |  ||||  || |    
AATGGCTCAAGCCGTTGAAGAATGGTACAAGCAGATGCCAATCATCACCCGCTCTTATCTCACCGCCGCAATCGTCACCACCATCGGTTGCTCTCTCGACgtatgcctctgtatctttcaggctttttcgatgtatcggtgtgcattattcttgtttattcccttgtgtggagggttgatagggttt--ttgttttcgatgt----

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|9259041|gb|BE347188.1|BE347188
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|9203644|gb|BE329868.1|BE329868
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|254322572|gb|GR837986.1|GR837986
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|213590246|gb|DB970086.1|DB970086
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|19453304|gb|BM954714.1|BM954714
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|213598283|gb|DB970167.1|DB970167
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|16348305|gb|BI973900.1|BI973900
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|254327112|gb|GR836721.1|GR836721
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
EST: gi|18733025|gb|BM527383.1|BM527383
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccct ... ggtgttgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgtaatcccctttcttcgcactctcacttttagggtttccaattttatttttttatgaattcggtgcgtctgatttgggtttattcttttttaatatctcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT