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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc...

Basic information

species Glycine max
transcript GLYMA09G41330.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 5'ss of exon 7
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatgga-aaaatggtcctcacaaattcc-tgccctagtaatcagtcctacatatggtc
||||| |||||||||||||||||||||||||||||||| || || || ||  | || ||||| ||||| ||||| |||||||||||||||||||||||| |||        |  |      ||||   |  |  |||||        ||| |  ||  |  | |  |||| |     | |               
GATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagt-tgagtccttgcatgc-----ctttttaggacgcctttcacatttgttatgttgttcttatgtcctgtgccttttgtgttaacag-----------

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 5'ss of exon 6
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgcccta-gtaatcagtcctacatatggtc
|| || |||||||||||||||||||| ||||||||||| || || || ||  | || ||||| ||||| ||||| |||||||||||||||||||||||| ||||      |  |    |||||||   ||   ||||| |  | | ||| |   |  |   || || | |  |   |  ||| | ||       
GACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagt-tgaa------tccttgcatgtttttttagg-atatttctttcacatatgttatgc-tattctcatgtcttgtgccttttgtcttccag------

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgc--cctagta---atcagtcctacatatggtc----------------------------------------------------
||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| || ||||| ||||||||| |||      |   |  |   || |  | |      | | | |||      |    ||  || || |    ||  ||   ||||||    ||| |   |                                                    
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagt-tgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G161418_T05 (Zea mays), 5'ss of exon 7
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcac----aaattcctgccctagtaatcagtcctacatatggtc
||||||||||||||||| |||||||||||||||||||||||||| || ||| | |||||||| ||||| ||||| |||||||| |||||||||||| ||   | |   |    | || |  |   |   || | | |  |       | |||  ||       ||     |  |  | ||  ||  || |       
GATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGTgtatgtccaagg---atggtttattttatcaccacagtaattcttttaccctttttgtctgcattcttggataatgacatttttcatttgttttatag------

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcag--tcctacatatggtc-----
|| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| |||||||| |||||||||||| ||        |||| ||    | ||||  |     |||||  |  |       |  |       |||   | | | | |     |  | ||| || |      
GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtc-------caatgattgcttattttggcatcacaatttttttta----cctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctgg--tgaatttcatgga--aaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc--
||||| ||||||||||| ||||| || |||||||||||||| ||||| ||  ||||||| |||||||| || || || | ||||||||||||||| ||||     |    ||  ||| |  |  ||  ||   || ||| |  ||  |||| | |   |  |    | |  |||     |||      | | ||||   
GATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGTgtgagtg-atcttaacttatacatttagtagtcaaggaccgacttttagagataaaaacgttgtgctgatggccattacctctctctcatattggcgtgtggttag

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtg---tgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc
||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||| |||||||||||||||||||||   | |||     | ||||| | |  ||    || |  |   ||  ||  | |  || |  | ||| | ||    | |||| |  | |        
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcatatatactt----gtaacatgggtgttaa--tcggtctgatga-ttcatacctctctcatcattgatgccag-----

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 5'ss of exon 7
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtg-tgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc-
|||||||||||||||||||| |||||||| |||||||| || ||||||||  | ||||| || ||||| ||||| |||||||| || || || ||||||| |||  |    |    |  |   ||   |  | | |||  || |||||||     ||   | |   |   |  |  | |  |  |  |  |  | 
GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGCgtaagtgatgacattgttttcggagttcaattatttatttatttttctgtaaaaatgtgaaccat--acttgggaagtcatgtttaaactaaggttggaaca

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: EFJ04980 (Selaginella moellendorffii), 5'ss of exon 6
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc
||||||||||| ||||||||||||||||| || || || |||||||| ||  || | ||||| || || ||  | || |||   |||||||| ||||||  |   | |  |  |||    | |   ||  |   |||   ||     |  ||   | |  ||  |||                          
GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGCgtaagt-cgtgcttcctttgtcacacttatactcttttctcttttgcgggtc--ttatcactaaagttttgtgcag------------------------

upper sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
lower sequence: EFJ36040 (Selaginella moellendorffii), 5'ss of exon 6
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc
||||||||||| ||||||||||||||||| ||||| || |||||||| ||  || | ||||| || || ||  | || |||   |||||||| ||||||  |   | |  |  |||    |     ||  |   |||   ||     |  ||   | |  ||  |||                          
GATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGCgtaagt-cgtgcttcctttgtcacacttacactcttttctcttttgcgggtc--ttatcactaaagttttgtgcag------------------------

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|254336235|gb|GR842414.1|GR842414
EST:     TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCCGGACTAATCTATCGCATGAAGCAACCCAAG
genomic: TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtga ... ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
EST: gi|254334604|gb|GR844389.1|GR844389
EST:     TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
genomic: TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtga ... ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
EST: gi|6951767|gb|AW423835.1|AW423835
EST:     CCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCCGGACTAATCTATCGCATGAAGCAACCCAAG
genomic: CCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtga ... ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
EST: gi|19270744|gb|BM887000.1|BM887000
EST:     CCCCATTCGACTTGAGGGTCTTGCCTATTCC-ATTAGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCCGGACTAATCTATCGCATGAAGCAACCCAAG
genomic: CCCCATTCGACTTGAGGGTCTTGCCTATTCCCATG-GTGCTTTCTCAAGTgtaagtgtga ... ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
EST: gi|6915664|gb|AW397194.1|AW397194
EST:     TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
genomic: TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtga ... ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
EST: gi|21887668|gb|BQ740881.1|BQ740881
EST:     TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCCGGACTAATCTATCGCATGAAGCAACCCAAG
genomic: TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtga ... ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
EST: gi|254334605|gb|GR844390.1|GR844390
EST:     TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT                         TATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG
genomic: TCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtga ... ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaat