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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgagagaacctttaccagttattttaacatattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC

Basic information

species Glycine max
transcript GLYMA10G41880.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g32570.1 (Oryza sativa), 3'ss of exon 4
gtgtgagagaacctttac--cagttattttaacatattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
|||  | |   | || ||   |   |   | ||  |||| ||   | | |  |   |||   ||       || |   |   ||||| |||||||    ||||||||    ||||| ||||||||||||| |||||| || || ||||| |||||||||||||| ||||| |||  ||||||   | 
gtgacatactgctttcactttaaccaaacttacccatttgagcctcttctctgtattcttg-atagacttgtattgtctg--tgcagTCTGCTAAGGAGGGTGAGCCATCTTGGGAGAGCCCTTGGGGTCGTGGAAGGCCAGGATGGCATATTGAGTGCAGTGCGATGAGCGCTCATTATTTGGGTA

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g04960.4 (Oryza sativa), 3'ss of exon 3
gtgtgagagaacctttac-cagttattttaacatattttagtaacatttgagatctct-catatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
         ||  || |     | || || | | || |     |||||     | ||| | ||| | |     || | |   | |||||||||||   ||| || |||  |||||| ||||| ||||| | ||| ||||| || ||||| ||||| ||||||||||||||||||  |||||||   |
-------gtaattttgatgttatgatattcatagatctcttgcacattgttactttctgcttatcttttctgtattattgtattcagGCTGCTAAGGAAGGCGAACCTTTCTGGGATAGCCCATGGGGCCGTGGTAGACCAGGATGGCATATTGAATGCAGTGCAATGAGTGCTCATTATTTAGGAC

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G874500_T03 (Zea mays), 3'ss of exon 4
-------------gtgtgagagaaccttt-----accagttatt--ttaacatattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
                |    | |  |||     || |  |  |   || | |||| | || || |||    | | || |||   |||||||  | |  || |||||||| ||    ||||| |||   ||||| ||||||||||| | ||||||||| || ||||| ||||| ||||| ||||||||||||   ||||||   |
gaactttaagcacaaatagctgtagttttctgaaacaaactgatatctagcttattgttgtcactttt----tttttcttatccttcaataaccattgttt-cagGCTGCAAAGGAGGGTGAACCTTTTTGGGATAGCCCTTGGGGCCGTGGAAGACCAGGTTGGCATATTGAATGCAGCGCAATGAGTGCTCACTATTTAGGAC

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G071924_T01 (Zea mays), 3'ss of exon 1
-------------gtgtgagagaaccttta--ccagttattttaacatat-tttagtaacatt-tgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
               |  | |  | || ||     || |  | |||  || | ||| |   |  | |  | | || |||   ||| |||  |    || |||||||| ||    || || |||   ||||| ||||||||||| | ||||||||| || ||||| ||||| ||||| ||||||||||||   ||||||   |
tttgtgaaactttaggcaaaaatagctgtagttttgtgaaataaactcatatctagcagtgtggtcacttttttcttatacttcattaaccat--gtttcagGCTGCAAAGGAGGGCGAACCTTTTTGGGATAGCCCTTGGGGCCGTGGAAGACCGGGATGGCATATTGAATGCAGCGCAATGAGTGCTCACTATTTAGGAC

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G56300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgagagaacctttaccagttattttaa--catattttagtaac-atttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
  ||  || ||  || | |  ||  || ||  | ||||| ||| |  |    ||| |      | ||     | | |  |   |||||||||| ||| | ||||| || || ||||| ||||||||||||| ||||||||| || |||||||| ||                                
--gtttgacaagtttaatctttttgttcaattcttatttcagttattaaactagagcagctggagtttatgctgaaatttttatgcagGCTGCAAAATCTGGTGAACCAAGTTGGGAGAGCCCTTGGGGTCATGGAAGACCAGGATGGCACATCGA--------------------------------

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G38830.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgagagaacctttaccagttattttaacatattttagtaacatttgagatctctcatattt---ctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
|| |||       ||| |   ||||| ||    |||| ||           || |     | |     |  |  |||| |   ||||||| || || || | |||||| || ||||| |||||||||||||| |||||||| || |||||||| ||||||||||||||||||| |  |||| |  |||
gtttgaatatcttttttctttttattatattcaatttgaggcttgcacagtatatgatgaagtgaagtttgaacataattctatgcagGCGGCAAAGCCTGATGAGCCAAGTTGGGAGAGCCCTTGGGGTCCAGGAAGACCAGGATGGCACATCGAGTGCAGTGCAATGAGTGTTCATTATCTGTCTC

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0265g00020.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgagagaacctttaccagttattttaacatattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
  |||||| |||  | || | || |  | | || || |  | |  |||| |    || |||||||  | |         ||||||||||| || || |||||||| || ||||||||||| ||||||||||||||||| || |||||||| ||||||||||||||||||||   |||||| ||  
--gtgaga-aactgtcacaaatt-tcctgatat-ttatgctcatttttgcg---cctaatatttccaatt---------ttgcagGCTGCAAAGCCTGGTGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCAGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgagagaacctttaccagttattttaacatattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
                    |  | | | ||| |||    | | ||||  | ||  |  |  | || | |  |  |   ||||||||||| || || | |||||| || ||||||||||| ||||||||||||||||| || |||||||| ||||||||||||||||||||   |||||| ||  
----------------gtgggcaactgtcacaaattgcc-tgatatttatgctcatttttcctcctaatttttccaattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT

upper sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S504_12V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------gtgtgagagaacctttaccagttattttaacatattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
                                                              |  ||   || |||  ||   ||   |      |  |  | | ||||    ||||| |   |      ||  |  |  | ||||  ||| ||||| || ||||||   |||||||| ||||||||||||||  | || || ||||||||||| |||||||| ||||||||     |||||  ||
gtcagcgcccttgaaaatggtgagagaaaactcttctgtctgctgagttaggtcctagggaattagactaaatcttgtcctactaaagtgggtgttggttctcaaattttctctctctgaaggtcgctggtatcattttctcgcagAGTGCGAAACCCGGAGAGCCTGCTTGGGACAGTCCTTGGGGTCCTGGGCGCCCGGGCTGGCACATTGAATGCAGTGCTATGAGTGCGGAGCATTTAGGTC

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|193637411|gb|FK584896.1|FK584896
EST:     TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAG                         GCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCT
genomic: TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAGgtgtgagaga ... ataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCT
EST: gi|193697128|gb|FK634812.1|FK634812
EST:     AGCTGTGGACTCAAGAAAGCGTCACCCAGACTGATTTTGCATTGTGGAAG                         GCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAA
genomic: AGCTGTGGACTCAAGAAAGCGTCACCCAG-CTGATTTTGCATTGTGGAAGgtgtgagaga ... ataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAA
EST: gi|193497894|gb|FK463380.1|FK463380
EST:     TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAG                         GCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA
genomic: TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAGgtgtgagaga ... ataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA
EST: gi|193693628|gb|FK633350.1|FK633350
EST:     TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAG                         GCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA
genomic: TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAGgtgtgagaga ... ataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA
EST: gi|193475805|gb|FK442530.1|FK442530
EST:     TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAG                         GCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA
genomic: TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAGgtgtgagaga ... ataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC
       tagtaac  putative branch site (score: 1)
                        tctcatatttctcaat  TA-rich tract