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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag

Basic information

species Glycine max
transcript GLYMA14G36540.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 10
CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag
|  | ||| || | || |||||||| || || ||||||||||||||  |||| ||  |||||||||| ||||| || ||||| |||||||||||||| ||||  |||||| |   |   | |   | ||  |   | |  ||  |||  | ||   | |   |||||||    ||||  |   |||||   
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtac-tgtatcttctttgcag--

upper sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 12
CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag
| |||||| || |  | || ||||| |||||||||||||||||| |  ||||||| |||||||||||||| || || |||||  |||| || || || |||||  |||||   | ||    |    |   |     || |  ||    |||  |  |  ||  ||| |  || || |              
CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttc-tctctagcccttaccct---ctcacacatttgtgtggtatctatta--ttctaaca--catgtttgt-tgcag-------------

upper sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 6
CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatct---ctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag
| |||||| || |  | || ||||| ||||| |||||||||||| |  ||||||| |||||||||||||| ||||| |||||  |||| || || || |||||  |||   | ||||  |        ||| | ||   ||||||      ||||    ||    |  |   ||                    
CACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTCAACATGGGATTGGTGCCGAGATATGgttcgtctagcccttaccctctcacacatttgtgtgtg-gtatctaggattttaataaatgatgcttgttgcag--------------------

upper sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 12
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 12
CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctcttta-cattgatttgtttttctatgaacgtatct-tactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag-----------------
| |||||  ||||  ||||||||||||| ||||||||||| | ||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||| ||||||||    |||||  ||   | |   | |   |||  ||    | |  | ||      || | |||| |     |  ||| || |||| ||  |                 
CCCTTGACAGATCGGCAATCAATGCTTCAGTCAGGAAAACTAGCAGACTGGTGACTGTTGAAGAGGGGTTCCCTCAACATGGTGTTGGCGCTGAGATCTGgttaccttctttttcaccaaatc--tatggcatgggcgagggtgtgatagtggtggtttag-aatcctccttttaagtatttttcttacaacgtgtctgaatttctgcag

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|120495804|gb|EH223971.1|EH223971
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|254335255|gb|GR846752.1|GR846752
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|254319589|gb|GR829101.1|GR829101
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCA-TGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
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|23735481|gb|BU766024.1|BU766024
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... 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|192320532|gb|FK011942.1|FK011942
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|11412033|gb|BF424044.1|BF424044
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... 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
EST: gi|151397384|gb|EV267257.1|EV267257
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
EST: gi|6848027|gb|AW350317.1|AW350317
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAAGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG