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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtcataaattgtatttatttcttgcttatggaaacatatataacttacactcattaccaatttctcgtgtatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

Basic information

species Glycine max
transcript GLYMA16G21340.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
gcaagtcataaattg-tatttatttcttgcttatggaaacatat---ataacttacactca----ttaccaatttctcgtgtattt-gcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
|  |    |   ||   | || ||| |  | ||      |  ||   || | || || |        |    ||| || || |||| |  ||||||||| | || ||||| || || ||||| ||||||||||| |||||||||||||| |||||||| |||||||| || |||||||| |||||||| || | ||
gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
-----------gcaagtcataaattgtatttatttcttgcttatggaaacatatataacttacactcattaccaa---tttc---tcgtgtatt-------tgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
             | |  ||   |||| || ||  | |   ||    ||  | |||  ||   |||  | ||  |   ||||   |  ||| ||       ||  ||||||||  |||| ||||| ||||| ||||| ||||| |||||||||||||| |||||||||||||| ||||||||||| || || || ||||| || || | ||
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
------------------------------------gcaagtcata--aattgtattt-----atttcttgcttatggaaacatatataacttacactcattaccaatttctcgtg----------tatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
                                    |   || |||  |||| |||||     |||  | ||||      |  | |  || |||   |||||     ||||   ||          | | ||  ||||||||| |||| ||||| ||||| ||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| || || || ||||| || || | ||
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
--gcaagtcata---aattgtatttatttcttgcttatggaaacatatataacttacac-tcattaccaatttctcgtgtatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
     | | |||   || ||| || ||||     | ||     | | | | | || |   |  |||| ||  ||   |   |||  |   ||||||||||| || || ||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| || || || || |||||    || | ||
gtattattgatatgtaactgtgttcatttacctttcat-----cctttgttattttcttgtggttactaacatcgttttccttttaa---cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
gcaagtca---taaattgtatttatttcttgcttatggaaacatat--ataacttacactcattac-caatttctcgtgtatttgcaat-gcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
||||||||   | |    | ||| ||     ||| |   |  | ||  || | |    |   ||     || | |  | | |||   || |||||||||||| ||||| ||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||||| ||||| ||||| || ||    |
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 18
gcaagtcataaattgtatttatttcttgcttatggaaacatatataacttacactcattaccaatttctcgtgtatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
                              ||  ||    | | | || |    |  |||| ||     | ||| | |   || ||||||||||||||||| || || || || || || || ||||| || ||||||||||||||||| || || || ||||||||||| |||||  |||| |  |
-----------------------------gtaatgatgtctctttgacgttattttgttactaa-----catgt-tctatcatccagTATTTGGTGCAATCGGCAGTCGACGGATACAACGTGTGCATTTTCGCTTATGGTCAAACTGGGTCCGGCAAAACATTTACAATATATGGTCCGGAAAATA

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 18
gcaagtcataaattgtatttatttcttgcttatggaaacatatataacttacactcattaccaatttctcgtgtatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
                              ||  ||    ||| | || |    |  |||| ||     | ||| | ||  || ||||||||||||||||| || || || || || || || ||||| || ||||||||||||||||| || || || ||||||||||| |||||  |||| |  |
-----------------------------gtaatgatgtctatttgacgttattttgttactaa-----catgt-tctgtcatccagTATTTGGTGCAATCGGCAGTCGACGGATACAACGTGTGCATTTTCGCTTATGGTCAAACTGGGTCCGGCAAAACATTTACAATATATGGTCCGGAAAATA

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|192306729|gb|FG998869.1|FG998869
EST:     TGAGGATACAAAG                         TATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTAT
genomic: TGAGGATACAAAGgcaagtcata ... tgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTAT
EST: gi|193524719|gb|FK480084.1|FK480084
EST:     AGTTTTTTGATGCTAATGCAACTCAAGAAAGCGTATTTGAGGATACAAAG                         TATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTAT
genomic: AGTTTTT-GATGCTAATGCAACTCAAGAAAGCGTATTTGAGGATACAAAGgcaagtcata ... tgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaacatatataacttacactcattaccaatttctcgtgtatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
             aacttac  putative branch site (score: 2)
     acatatataactta  TA-rich tract