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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaactgatgaggtttttttttaattattattattcacgctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC

Basic information

species Glycine max
transcript GLYMA11G05830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 2
gtattcttactttcttctttaattatccaa--aattgcttcttttttttttttttgtagtatagatat----------gaacttttgaactgatgaggtttttttttaattattattattcacg-ctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
|||  ||             ||||  | ||       |||||||||||| |||   |  | | | | |          || | ||   ||  |     |    |  ||    || ||      |    ||| || ||||| |||||||||||||||||||| || || ||||||||||| ||||| || ||||| ||    || |||||  ||||||| ||  | ||||||
gtacactacacacaccacgcaattgccaaatcgccgccttcttttttttctttcctttttttggctgttctcttaccagatcattcctacctacctactccgatcctaccatttcttgcctgtgatctcagGATACTTGTGTATGAGTACGTGGACAATGGCAACTTGGAGCAGTGGCTTCATGGCGACGTTGGACCGGTTAGCCCTCTGTCTTGGGACATCAGGATGAAC

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g34430.1 (Oryza sativa), 3'ss of exon 2
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaactgatgaggttttttttt---aattattattat-tcacgctg--cagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
                              | || |||   | |     || | | |||    | |  | ||   || | |  ||||||  |  |   |||  |  |||| |  | |||  ||| |||||||| |||||||| || ||||| || ||  ||||||||||||| |||||||| ||||| |||   || |||||  | |||||     |  |||| 
----------------------------gtattttcttgcatgtgcacattatttggtaaccttgttgaattgcaaaatcaaaaggtttgataatgtaaatggtgtttatgtggctctgaccagGATGCTTGTGTATGAGTATGTCGACAACGGGAACCTAGAGCAGTGGCTCCATGGGGAAGTTGGACCTGTAAGCCCTCTTTCGTGGGATTCCAGGGTGAAG

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G040964_T01 (Zea mays), 3'ss of exon 2
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaactgatgaggtttttttttaattattattattcacgctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
       || | |||| |    |      |||   ||| |||   || |||   |  || | |||  ||  |           || | ||  ||   |  || || |        ||| |||||||| |||||||| || || ||||| || ||||| || |||||||| ||||||||||||||  | || |||||  | |||||     | ||||| 
------gta-tgtcttgtcaggtgtgtgcaaaccacttgtttcgcttgtttggctgataca-atactaatgt-----------agatgttggttctgtgtttcttgt--------cagGATGCTTGTATATGAGTATGTTGATAATGGGAACTTAGAACAATGGCTGCACGGGGATGTTGGGCCCAGAAGCCCTCTCGCCTGGGATGACAGGATGAAG

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 2
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagat---atgaacttttgaactgatgaggtttttttttaattattattattcac-gctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
          | |||||||    |||  | ||| |||| |   || | || |   | ||||||    | ||  || |    | || |    |||  ||   |||  || ||  |   | ||| |||||||| |||||||||||  | ||||| || || ||||| ||||| |||||||||||||| |||   || ||||| || ||||| ||  ||||||| 
---------gtatcttcttg---tatggacaatagctt-tagcttatattgtgaaattatagaaccaaggagtttgtagctttatcataaatttcattgtatatggttcttttccattccagGATGCTTGTGTATGAGTACGTTAATAATGGAAACTTGGAGCAATGGCTCCATGGGGATGTTGGCCCTGTGAGCCCTCTTACATGGGATATCAGAATGAAG

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------gtattcttactttcttctttaa--ttatccaaaattgcttcttttttttttttttgtag--tatagatatgaacttttgaactgatgaggtttt--tttttaattattattattcac-gctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
                                                              | || ||| || |   || ||  | ||      ||| ||  |||||||||  | |  |    || | ||||  | || ||| |||  | |  |  | |   ||  || ||     | | || || |||||||| |||||||| ||  | ||||| ||||| ||||||||||| ||||| ||||| |||||| | |||||||| |||||||| ||||||||||| 
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaactgatgaggtttttttttaattattattattcacgctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
                  | ||  ||  |   ||  | |    |    ||||||| ||      |  |   | | |   |   |    |   ||    | |  |   |     || || |||||||| || ||||||||||||||||| ||| | ||||||||||| |||||   | |    |     |   | ||  | ||||||  ||| |||   
-----------------gtgaagcattta---ttcttcccacctggagtttttgt-gtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggctt---ttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 2
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaactgatgaggtttttttttaattattattattcacgctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAG-TCCTCTAACTTGGGAAATTCGAATGAAC
                   | | | ||    ||  ||||||  |      ||||| || | |    | |  |      |||||   ||| ||        || |  |    | ||||| |||||||| || ||||||||||| ||||| || || |||||||||||||||||   |  ||  ||   ||  | | ||  | ||||||   || |||   
------------------gtgaatgtc----atcccttcttcctgcccagtttgttgtgtggtggcgcagctcc---ttgatgttctttgttgacctcgtttctggtggctgttgcagGATGCTTGTGTACGAGTACGTGGATAATGGAAACTTGGAGCAGTGGCTGCATGGACCT-CTGTCCCAAACAAATACACTTCCATGGGAAGCCCGCATGCGG

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ27863 (Selaginella moellendorffii), 3'ss of exon 3
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaa-ctgatgaggtttttttttaattattattattcacg-ctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
                                                                  | || |   |  || ||||     ||||| | ||   || |   ||  || ||| ||||| || ||||||||||| |||||||||||| | ||||||||||| || ||    |       |  ||   ||| ||| |||||  || | ||||| 
------------------------------------------------------------------gtacgtcgaattctcatgaaagagtttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAGGTTAGGATGAAA

upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaa-ctgatgaggtttttttttaattattattattcacg-ctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
                                                                  | || |   |  ||  |||    |||||| | ||   || |   ||  || ||| ||||| || ||||||||||| |||||||||||| | ||||||||||| || ||    |       |  ||   ||| ||| |||||| |||| ||||| 
------------------------------------------------------------------gtacgtcgaattctcgtgaaagattttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA

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|13481467|gb|BG510810.1|BG510810
EST:     ACCAA-TCCTTAGTCAGGTTGCTTGGTTATTGTGCTGAAGGAGCTCATAG                         AATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCA
genomic: A-CAAGAATTTAGTCAGGTTGCTTGGTTATTGTGCTGAAGGAGCTCATAGgtattcttac ... cacgctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaacttttgaactgatgaggtttttttttaattattattattcacgctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
                            ttttaat  putative branch site (score: 3)
               tgatgaggtttttttt  TA-rich tract