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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttagatattgttgtgaatttcttcaaatacaggatctatacatcttgatcttatatatatatatgccttttgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT

Basic information

species Glycine max
transcript GLYMA15G41690.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
-----gtatgcttagat--attgttgtgaatt---tcttcaaatacaggatctatacatcttgatcttatatatatatatgccttt---tgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT
     ||| | | |  |   ||  ||| ||||   | ||   |   ||| | |  | |     |  ||     | |  ||||   |   | |  || ||||| ||| | || || || ||||||||||||||||| |||||||||||||| ||| | ||||||||  | ||||| | |
agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT

upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G128114_T03 (Zea mays), 3'ss of exon 9
gtatgcttagatattgttgtgaatttc---ttcaaatacaggatctataca-tcttgatcttatatatatatatgccttttgaa---------cttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT
 | |  ||  | || ||  ||  ||     ||   || |    ||  | || |||    | | |  ||    ||||      ||          ||  |||| ||| | ||||| || || |||||||||||||| |||||||||||||| ||| | |||||||| || ||||| | |
atttttttgaacatagtcttgttttgaaggtttgtatgctctgtcatttcagtctgagaccttttaatgatgatgctcacaaaaaataattattttttagGTCTCTTTGGAACTTGGTGGGAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCTGTTAAAGGCAGT

upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 10
---------gtatgcttagatatt---gttgtgaatttcttcaaatacaggatctatacatcttgatcttatatat-atatatgccttttgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT
           ||| |    | ||   | | || ||    |   ||    |    | || |  ||||  |    |  | | |       | |  ||  |||| ||  | ||||| || || |||||||||||||| ||||| |||||||| ||| | |||||||| || ||||| | |
gttttttgaacatggtcttgttttgaaggtttgcatgctctgtcatttcagtctgagacctagtgatgatgctcaccaaaaaaaaacaataatgttgtagGTCTCCTTGGAACTTGGTGGGAATGCACCTTGCATTGTTTTCGATGATGCGGACATTGATGTTGCTGTTAAAGGCAGT

upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv19s0085g00870.t01 (Vitis vinifera), 3'ss of exon 9
gtatgcttagatattgttgtgaatttcttcaaatacaggatctatacatcttgatcttatatatatatatgccttttgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT
|||||| |||||  | |   ||||||     |  |  |   || || |  |  || | ||  || |   |   |  |||  ||| |||||||||||||||  ||||| ||||||||||||||||||||||||||  | |||||||  || |||||||||  || |
gtatgcatagat--tatca-gaattttccagagaaatgagcctctagaaatc-atgtcattaatttccttcaatcatgactttctagGTATCTCTTGAACCTGGCGGTAATGCACCTTGCATAGTTTTTGATGACACGGACCTGGGCGTGGCAGTAAAATCAATT

upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv19s0085g00880.t01 (Vitis vinifera), 3'ss of exon 10
gtatgcttagatattgttgtgaatttcttcaaatacaggatct-atacatcttgatcttatatatatatatgccttttgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT
       | |  || || |  ||||  |  |   ||| |   | | | ||| | || || |  ||     |     |     ||| |||||||||| ||||| || || ||||||||||||||| | ||||| ||||| |||||||| || |||||||||||  ||
------gttggcatagtag-aaattgttaaaggaacaagccttcagagatcattatattgttaattgccttaatcataatttttctagGTATCTCTGGAACTTGGTGGTAATGCACCTTGCATAATCTTTGACGATGCAGACCTGGAGGTGGCAGTAAAAGGGGCT

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|209725352|gb|BW651520.1|BW651520
EST:     CGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAA                         GTATCTCTTGAACTCGGCGGCAATGC
genomic: CGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAAgtatgcttag ... gaacttccagGTATCTCTTGAACTCGGCGGCAATGC
EST: gi|151400125|gb|EV269939.1|EV269939
EST:     CGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAA                         GTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCT
genomic: CGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAAgtatgcttag ... gaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCT
EST: gi|151404401|gb|EV274211.1|EV274211
EST:     CGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAA                         GTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCT
genomic: CGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAAgtatgcttag ... gaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacaggatctatacatcttgatcttatatatatatatgccttttgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT
                tcttgat  putative branch site (score: 4)
                                       ccttttg  putative PPT
          tatacatcttgatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttagatattgttgtgaatttcttcaaatacaggatctatacatcttgatcttatatatatatatgccttttgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA