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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG

Basic information

species Glycine max
transcript GLYMA17G11220.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
                                                  |   |   |     |  |  || ||    || ||    |    | ||   || || |    || | || |||  ||     |  |||| ||||||||| | ||||||||||| ||||| ||||| ||||| || ||||| || ||||| |||||||| || |||||||| || ||| |
-----------------------------------------------gtaagcttgtcttccctgcaaggattattgtgtttactcaaagttctgtttcctagaactaaaagacttattttccctg-----tacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG

upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
                                                   ||   ||  || |     |||  |  | |||    | |    ||   |||  ||  || | |   || ||   |  |||||  |||||||||||||| | |||||||| || ||||| ||||| ||||| || || || || || || || ||||| |||||||| || ||||||||
--------------------------------------------------gtaggtctatttca--ccaaattgtttg-ttgtttactaaagtttggttttggaacactgtaa---atatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG

upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttc---tatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
                                                 |||      | || | || |  |  || | ||    |  |   | || || |   ||  ||| | | || |     |||| ||  |  |||| ||||| ||||||||||| || |||||||| ||||| |||||||||||||| || ||||| || ||||| |||||||| || ||||| ||
------------------------------------------------gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG

upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttcttaccttcctaaactgtttgtattag-----atcgcaaatttctactatactacttgttgaggta----taatcat--aagct--tgacctccatcaattttctttacaag--------tctctgattcatgttctatggtctc-----tttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
||||||| ||    | ||  |   | |||  |       ||  ||| | ||||      |  || |  || ||    |  |||    |||   |||  |   | || || | | | ||         | ||||| |     |  |   |||      || ||||||| |||||||| |||||||| || ||||| ||||| ||||||||||||||||| ||||| |||||||| || |||||| |||| |||||
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG

upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S355_49V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttct-actatac--tacttgttg-aggtat--aatcat--aagcttgacctccatcaatttt----ctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
                         ||| ||| ||| |||      |   |   || |     || || |||  ||  | || |||  |  ||   || |||  | |       |     ||| |       |||  |||| || |  | |||    |         || | |||||||| ||||||||||| ||||||||  | || ||||||||||||||||||||||| ||||| || || ||| | || ||||||||
gtatgcaattttacatttgccccgtgtttttatctttctaccaaactctcacctgagcatgttttgcttactgaacgtttctcgtttcacatagcaaaccatctatggcaagtgttttgaaatatcgaaatgttaatagtcgcttacacctgtgtcctaaatca--cagAGAGAGTTTTACCTTGAAGGAGGTGCTATGGTTCTTGCTGATGGAGGTGTTGTCTGCATTGATGAGTTCGACAAAATGCGACCTGAAGACAG

upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ31205 (Selaginella moellendorffii), 3'ss of exon 10
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
                                                                    ||  | |  |  | |   | |||  ||    ||     | | | |||||  || |||| | | |  |||| ||||| ||| | || ||||| || |||||  | ||||||||||| || || ||||||||||| ||||| ||||||||||||||||||||
-------------------------------------------------------------------gtaggcttccg--taaatgctatctgttccacttgttt-tttttcattcaatttgtatgatgt-tccagCGAGAGTTCTATTTAGAGGGAGGAGCGATGGTGCTTGCCGATGGAGGGGTGGTTTGCATTGACGAATTTGACAAGATGAGGCCAGAAGACAG

upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ17142 (Selaginella moellendorffii), 3'ss of exon 10
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
                                                                    ||  | |  |  | |   |||||  ||    ||     | | | |||||  || |||| | | |  |||| ||||| ||| | || ||||| || |||||  | ||||||||||| || || ||||||||||| ||||| ||||||||||||||||||||
-------------------------------------------------------------------gtaggcttccg--taaatgccatctgttccacttgtt--tttttcattcaatttgtatgatgt-tccagCGAGAGTTCTATTTAGAGGGAGGAGCGATGGTGCTTGCCGATGGAGGGGTGGTTTGCATTGACGAATTTGACAAGATGAGGCCAGAAGACAG

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|7924143|gb|AW830169.1|AW830169
EST:     AGATAGCGGCACT                         CGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTT
genomic: AGATAGCGGCACTgtaagttctt ... gtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
                          ctctgat  putative branch site (score: 4)
                                              tctcttt  putative PPT
       atcaattttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG