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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA

Basic information

species Glycine max
transcript GLYMA14G36540.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 12
---gtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA
      | |||||  ||||  ||| |     || ||   | ||        |||  ||| | || || |            ||   |||||  |||  |||||  |||| ||||| ||||  |||||||||||||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||| || || 
gtacgctctctctccacatgcattggcacacctgtgtgtggataaggacttttagttct-gacactcgt------------tttctttgca--gCATGTCTGTTGTTGAGGAAAGCTTTGAATATCTTGATGCACCAGTTGAGAGAATTGCTGGAGCTGATGTACCCATGCCCTATGCTGCCAATCTTGAGAGG

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 10
gtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA
||  |||||| |   |   | |   | ||  |   | |  ||  |||  | ||   | |   |||||||    ||||  |   |||||  |||  |||||  | || || || ||||  ||||||||||| || |||||||| |||||||| |||||||| |||||||| || || || || || || || 
gtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtac-tgtatcttctttgca--gCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 11
gtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA
||    | || | | |   |   |  |||    || ||||   | ||  ||      | |  || ||   |  || | |   | |   |||||  |||||  | || || || ||||  |||||||||||||| || ||||| |||||||| |||||||| |||||||| || || || || || || || 
gtcggccactctccctccctccctccttccc--aatgtat---aatgtatagtctgcgtctctcgtaatgggttgaaatgtgcctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGG

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 12
gtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtg-tacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA
                      ||| |     |  | || | |       |  | |  |  ||| ||| | | |   || | | |    |||||  |||||  | |||||||| || |  || ||||||||||| |||||||| |||||||| |||||||| || ||||| ||||| || || || || |||
----------------------gttctctctagcccttaccctctcacacatttgtgtggtatc-tattattctaacacatgtttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGA

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 13
-----gtttatctctttacattgatttgtttttctatga--acgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA
      || |  || ||| ||| | | |   |  ||| |  || |   ||      ||  | |     |     | |   | | |     | |  |||  | || ||  | ||||| || |||   ||  | |||||||| || ||||| ||||| || ||||||||||| ||||| |||||||| || || || |||
gttaacttcaattcctta-attcaatagagatcttattatcacctggattgtataatagttttaaaacacggattaaactttttccgtaatggatcagTGCGTCGGTTGTAGAAGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGA

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 12
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
gtttatctcttta-cattgatttgtttttcta--tgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctc-------------ttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA
|||    |||||  ||   | |   |    |    ||  || |  || ||||    |     |   | | | ||| | |   |  |             ||   ||| |  ||||| ||||| || || |||| || |||||||||||| || || || ||||| ||||| ||| ||||||||||||||||||||||||| || |||
gttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA

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|120493945|gb|EH222112.1|EH222112
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|19053203|gb|BM731870.1|BM731870
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|9439950|gb|BE440462.1|BE440462
EST:     GTGACAGTGGAAGAAGGGTTTCCTCAGTATGGCGTGGGCGCTGAAATCTG                         CCGCATC-GTCATTGAA
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCA-CATCTGTCATTGAA
EST: gi|207761269|gb|GD733682.1|GD733682
EST:     CAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: CAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|298169681|gb|HO021041.1|HO021041
EST:     TGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: TGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGC-TGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|17962851|gb|BM269607.1|BM269607
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|5606648|gb|AI900746.1|AI900746
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGA
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGA
EST: gi|254334369|gb|GR844154.1|GR844154
EST:     TGACAGTTGAAGAAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: TGACAGTTGAAGAA-GGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|10845821|gb|BF068863.1|BF068863
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|9565969|gb|BE475478.1|BE475478
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA
          ggttaac  putative branch site (score: 3)
                                       tacttctctt  putative PPT
                        aatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT