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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG

Basic information

species Glycine max
transcript GLYMA18G51810.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
----------------gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaa--gctttatagtttcat--tccttaat--tatgc----ttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
                |  || |  ||  | | ||  ||||   |   ||| |||  |      |  || ||  |||      |||| |  | | ||||   ||||     | |  | |||||||||||||||| |||| || |||||||||||||||||||| |||||||| || ||||| || ||||| || ||    || ||  ||
gtacaaatatttaccagaaatctgttgcatctattttatttagata-gatttatattacaggaatttttgaatagctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 13
gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
  |||  | |    | ||     |  | ||   |||||     ||   | |||  |  |||    ||| | |       | |  || |    |||||||||||||||  | || |||||||||||||||||||| || |||||||| ||||| || || || || || ||    || ||   |
-gtatg-agtacaatattgaagatgatattgtcttcatgtc--gaatataattcgatatttcctatttaagtgacaccatctattttttga-gcagGCAGAGAGTGCAATAGATCAAATGGATTGGATTGAAAAGATTACTGGTGTCATTGCATCTTTGCTTAGCTCACAATCCCCAGAACAG

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 13
-----------------gttatttaatgtgt-tttttggatttttttttaattcatacaaggatggtgattaaagct--ttatagt-ttcattcct---taattatgcttgtcag------tgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
                  |   || || | | ||| |  ||      | |  | |||  | | || | | || |  |  || |  | || ||| ||   || | |||    |  |      ||||||||||||||||  |||| || |||||||||||||||||||| || || || |||||||| || ||||| || |||  ||||||  | 
gtatgaagcttaaatgcatatgttgatatctgtttctttatacaggatgatgttatatgaagctgttcaatagacatacttgtgatattgatttctgtctagtgatgtgcattggaaattgtgcagGCAGAGAGTGCAATGGATCAGATGGATTGGATTGAAAAAATTACCGGCGTCATTGCTTCTTTGCTGAGCTCCCAGTCTCCTGAACGA

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
  ||    |  ||||| | |   |    | |   | ||     |||  |||||||   || |    | |||      ||  ||||  | | ||||||||||||||||  | || || ||||||||||||||||| || ||||||||||||||  | || ||||  || ||    || ||   |
-gtacaccacatgtttatgg---tgcagtctgccttatt----gattctgattaagatttcaatactccatgaacacatc-tgctattta-tgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
gttatttaatgtgttttttggatttttttttaattcat-acaaggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
               | | | |    ||| |  |   | | |  ||   |||| ||  |||      |||||      ||  ||||  | | | ||||||||||||||  | || || ||||| ||||||||||| || |||||||||||||| || |||||||| || ||    || ||   |
--------------gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatc-tgctattta-tacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 13
--gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaagctttatagttt-----cattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
   | ||| |  |||||| ||      ||      ||  |  |   ||| |     ||| || |||||||     || |  ||| ||||| |||||||||||||| |||||||| || || |||||||||||||| ||||| |||||||| |||||||| ||| |||| ||||||||| | |||||   |
gtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagttttcactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------------------------------------------------gttatttaatgtgttttttggatttttttttaattcata------caaggatggtgattaaagctttat--agtttcattccttaat--------tatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
                                                                              ||  || ||| ||| | || | |  |  |  | |  |        |||  |  | ||| |   |||    | |     || |||||        | ||||||||||  |||||||||||||| |||||||||||||||||||||||||| || || || |||||||||||||||||||||||||||  |||||| |||
gtaaatcttacagcttaggttgcactcatgaagttcagtttacttctttgaaattatttgatacctgaaactgtatttttgcttgatg-gttctgtgaaatactgatggaatggtgaattgttaagtgttattattgatttttttctcactagtgctcattaatgttgtacatttgcttgtcagcacagGCAGAGAGTGCACTGGACCAAATGGATTGGATTGAAAAGATAACAGGGGTTATTGCTTCATTACTGAGTTCTCAGGCTCCTGAGAGG

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|21637852|gb|BM108007.1|BM108007
EST:     TGAGGTTTTGCTTCCGGATCATTTCACCTACAAAGAACTACACTTTGCAG                         --ANAG--TGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTT
genomic: TGAGGTTTTGCTTCCGGATCATTTCACCTACAAAGAACTACACTTTGCAGgttatttaat ... gtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
                               ccttaat  putative branch site (score: 4)
         attaaagctttata  TA-rich tract