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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaagaataacatgtgccattttgttatctttatgctactgttgtgataaagcaattatctctagttacggtatggtgtag

Basic information

species Glycine max
transcript GLYMA15G12780.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 3
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaagaataacatgtgccattt----tgttatctttatgc-tactgttgtgataaagc--aattatctctagttacggtatggtgtag------
||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||| |||||  ||||  |||| |  |  | |||      | |       | | |||||   || |||| |  || | |   || |  | || |  | | || |   ||      
CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAGgtcagtagcagaacaatcatcctttgtatgcatcaatttttttatatatattgtttttttataactgtatgaattataatc-cagaattgcacaggcattg

upper sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g50050.1 (Oryza sativa), 5'ss of exon 4
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgt--agaaagaataacatgtgc-cattttgttatctttatgctactgttg-tgataaagcaattatctctagttacggt-atggtgtag-------
|||||||| |||||||| ||||||||||| || ||||||||||| || || || || ||  | || || ||||||||  | ||||||||||||  || | || |||| ||| | |||     | || || || |||||| | |  |  ||   |  |     |||| | |  |  |  |        
CTTCAGGCCTATTTTCTGGTTCTTGATGATATAATGGATAACTCACAAACTCGACGAGGAAAACCCTGTTGGTTTAGGCTTCCCAAGgtttgtcaagtaggattaacttgtccacatagaaatgtccttgtgttactgtagattctcgagtgttgttaaaatgttatgattgtactccaactaaaca

upper sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g50050.2 (Oryza sativa), 5'ss of exon 3
-------------CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgt--agaaagaataacatgtgc-cattttgttatctttatgctactgttg-tgataaagcaattatctctagttacggt-atggtgtag-------
             |||||||| |||||||| ||||||||||| || ||||||||||| || || || || ||  | || || ||||||||  | ||||||||||||  || | || |||| ||| | |||     | || || || |||||| | |  |  ||   |  |     |||| | |  |  |  |        
GAGTAACCTGCAGCTTCAGGCCTATTTTCTGGTTCTTGATGATATAATGGATAACTCACAAACTCGACGAGGAAAACCCTGTTGGTTTAGGCTTCCCAAGgtttgtcaagtaggattaacttgtccacatagaaatgtccttgtgttactgtagattctcgagtgttgttaaaatgttatgattgtactccaactaaaca

upper sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 3
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaagaataacatgtgccattttgttatctttatgctactgttg-----tgataaagcaattatctctag--ttacggtatggtgtag-------
||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| ||||| ||||| |||||||||||||||||  ||||| | |  | ||    | | | |  |||  ||| |    |  | || |||     || |        | |    ||  ||||  | |    | |       
CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttag-atcaggagcgtc-tatcctttttacttaccaaattatttctattgattcttgctttgatggctgtactaagtcttacactctcacttgggaagttt

upper sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 3
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttg-tagaaagaa--taacatgtgccatttt----gttatctttat--gctactgttgtgataaa-gcaattatctctagttacggtatggtgtag--
||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| ||||| || || |||||||||||||||||  ||||| | |   ||| |  || | | |   | ||      |||| | |||    |  |||| ||||    | | | |  |||        ||     ||   
CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAGgttagatcagaagcatctatccttttttacttaccaaattatttctatcaattcttgttttgatggttgtactaaggtcttacactcttacttgataagt

upper sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaagaataacatgtgccattttgttatctttatgctactgttgtgataaagcaattatctctagttacggtatggtgtag
|| || || ||||| ||||| |||||||| |||||||||||||||  ||| ||||||||||| || |||||||| ||||| ||  ||||    ||     |||   | || ||   ||   ||   |    ||| || | | | |    |||                       
CTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAGgt--aaagttttcatattttttgtcacgctgcagtc--cactagactattctaacacaatg-ttacag--------------------

upper sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 4
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaagaataacatgtgccatttt---------gttatctttatg-ctactgttgtgataaagcaattatct--ctagttacggtatggtgtag
||||| |||||||| ||||| |||||||| |||||||||||||| || ||||| || ||||| || |||||||| || || ||||||||        | | | ||   |    | ||            || |||     | |   | ||||||||  |    ||  ||   |  | | ||   |||
CTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAGgtgcaagcctatagtgaccctttttttctttacagtgcaagcatgtttgcaattgccactttgataaagtgaagtactaactttcttagatttgtcttag

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|298187383|gb|HO034532.1|HO034532
EST:     ATAACTCTCGCACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|298187020|gb|HO034169.1|HO034169
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|13789758|gb|BG652349.1|BG652349
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|9902003|gb|BE610971.1|BE610971
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|192294520|gb|FG987449.1|FG987449
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|19345889|gb|BM890769.1|BM890769
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|298181906|gb|HO026081.1|HO026081
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTACAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|7233280|gb|AW568628.1|AW568628
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|5606131|gb|AI900229.1|AI900229
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|193581203|gb|FK535486.1|FK535486
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|208272802|gb|GE066266.1|GE066266
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTA
EST: gi|15814471|gb|BI786746.1|BI786746
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|9565120|gb|BE474629.1|BE474629
EST:     GGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: GGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|208045687|gb|GD838961.1|GD838961
EST:     TCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: TCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|14259182|gb|BG882090.1|BG882090
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|208302800|gb|GE097933.1|GE097933
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|6071532|gb|AW100919.1|AW100919
EST:     ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaagaataacatgtgccattttgttatctttatgctactgttgtgataaagcaattatctctagttacggtatggtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG