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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttttttccccaaatgagtattgcagacagcagcattgcttttgaagcatttttttttattttttgtgacttaatatgatttcttttgtactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGAGCATCAGGGGCAAACATCAGCTACATCCGTCGAGCTAGTGGAGCAAGTA

Basic information

species Glycine max
transcript GLYMA10G03910.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G03910.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g42900.1 (Oryza sativa), 3'ss of exon 5
gtatccttttttccccaaatgagtattgca-gacagcagcattgcttttgaagcatttttttttattttttgtgacttaatatgatttcttttgtactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGAGCATCAGGGGCAAACATCAGCTACATCCGTCGAGCTAGTGGAGCAAGTA
||    |||| |  |    ||||     || || || |   ||   ||| ||    |  ||           |    | |||||  | | |  ||   |   |||| |||||  |||||||||||||| | |||||||| |||||||| ||||||||| | || || |  || ||||| || ||| |    ||||| ||||   
gtcagtttttgttgcactttgagctaaacacgatagtacttttatctttaaaatgctaattcacgaggcagcta--ctgatatg--tgcatccgtcaaa---agGTTACACACAACATGCAAATTCCTCTCTCCTATGCTGATGCTGTGATTGGAGCAGCTGGTGCTAGTATTAGCTATATTCGTAGGCACAGTGGTGCAACAG

upper sequence: GLYMA10G03910.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0141g00800.t01 (Vitis vinifera), 3'ss of exon 5
gtatccttttttccccaaatgagtattgcagacagcagc-attgcttttgaagcatttttttttattttttg-------tgacttaatat--gat-ttcttttg-----tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGAGCATCAGGGGCAAACATCAGCTACATCCGTCGAGCTAGTGGAGCAAGTA
                 ||  ||  |||||  |||   | |||  |||   | ||||  |    ||||||||       |||||| || |  ||| ||  | ||     |  | ||||| |||||||  |||||||| ||||| | || |||||||||||||| ||||| ||||| || | ||| || |||||  | || ||  | ||||| |||| ||
-----------------aagaag--ttgcaagcagttcctattattttcacaacattggtcacaattttttgacatatctgactttatgtttgatgttgctgtggtggttgttctgtagATCACACAGTACATGCAAGTTCCTCTATCATATGCAGATGCTGTAATTGGGGCATCTGGTGTAAATATAAGCTATGTACGCCGTACCAGTGGGGCAACTA
















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|8282513|gb|BE020004.1|BE020004
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|254323299|gb|GR840104.1|GR840104
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATTTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|17963169|gb|BM269921.1|BM269921
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|31460923|gb|CD402951.1|CD402951
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|9902211|gb|BE611179.1|BE611179
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|51337757|gb|CO981623.1|CO981623
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|18734549|gb|BM528247.1|BM528247
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|254323298|gb|GR840103.1|GR840103
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAA                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
EST: gi|17401691|gb|BM178473.1|BM178473
EST:     TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAG                         GTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA
genomic: TGGGAATTCATTCATCCAGTGCACAGGCACAACAATCTGTTGTGACTAAGgtatcctttt ... tactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagcatttttttttattttttgtgacttaatatgatttcttttgtactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGAGCATCAGGGGCAAACATCAGCTACATCCGTCGAGCTAGTGGAGCAAGTA
                         acttaat  putative branch site (score: 4)
                                    tttcttttgt  putative PPT
     atttttttttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttttttccccaaatgagtattgcagacagcagcattgcttttgaagcatttttttttattttttgtgacttaatatgatttcttttgtactatgtagGTCACACAACACATGCAAATTCCTTTGTCCTATGCAGATGCTGTTATTGGAGCATCAGGGGCAAACATCAGCTACATCCGTCGAGCTAGTGGAGCAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG