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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatactggcacacccatgttactctaatacatttcactatgaacttgagaaaaatatatttcaatatctaatttctttctttcctttttattattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGATCGTGTCAGAAATTTGTATTTCACTTTTCTCTTTGTTCTGCGAGCAGTAA

Basic information

species Glycine max
transcript GLYMA15G23150.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G23150.3 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 5
gcatactggcacacccatgttactctaatacatttcactatgaacttgagaaaaatatatttcaatatctaatttctttctttcctttttattattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGATCGTGTCAGAAATTTGTATTTCACTTTTCTCTTTGTTCTGCGAGCAGTAA
              |||  |||  ||  |    || | | |  | |     || ||  ||   | | | |       ||||    |    ||  |  |||||||||||||||||| ||||| |||||||||| ||||| |  ||||| || ||||||   ||| |||| ||||| |  || |||||||| || || || |
------gtatgtgaccagattatcctcctttgctt-attgtttattgtgccaagatgcata--attgttttgaccacttctaatgtaaaaatggtcacagTGGGGACAAAATCTTCCTTTGTTGTATGACCGCGTCCTGAAGTACCCAGAACGTGTCCAGAATCTGTACTTCACCTACCTGTTTGTTCTTCGGGCCGTGA

upper sequence: GLYMA15G23150.3 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 5
gcatactggcacacccatgttactctaatacatttcactatgaacttgagaaaaatatatttcaatatctaattt--ctttctttcctttttattattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGATCGTGTCAGAAATTTGTATTTCACTTTTCTCTTTGTTCTGCGAGCAGTAA
                |||| ||   | ||   | |   || |  ||           | ||   ||  || |||  |    | |  | |  ||  |  |||||||||||||||||| ||||| |||||||||| ||||| |  ||||| || ||||||   ||| | || ||||| |  || |||||||| ||||| || |
--------------gtatgtgaccgaattatcctccttcattattttttattgtgccaagtttcgtaattattttgaccacttctaatgtaaatggtcacagTGGGGACAAAATCTTTCTTTGCTGTATGACCGTGTCCTGAAGTACCCAGAACGTGTCCAGAATCTATACTTCACCTACCTGTTTGTTCTTCGAGCCGTGA

upper sequence: GLYMA15G23150.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 5
---gcatactggcacacccatgttactctaatacatttcactatgaacttgagaaaaatatatttcaatatctaatttctttctttcctttttattattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGATCGTGTCAGAAATTTGTATTTCACTTTTCTCTTTGTTCTGCGAGCAGTAA
   |     |        | || || |        |||   ||| ||  |||      |  ||  || |||||||      | |||  | |||  | |  |||||||| |||||||| || ||| | |||||  ||||| ||| |||||| || |||||| |||| ||||| |||||||||||||||||||| ||||| |  |
cttgtcctttctttttttcctggtatttcttgcattttttttattaatatgaagtctgttgatgaca-tatctaacaataattttttttctttgctgt--cagTGGGGTCAAAATCTCACATTGCTCTATGATAGAGTCATAAAATACCCAGACCGTGTCGGAAACTTGTACTTCACTTTTCTCTTTGTTCTTCGAGCTGCCA

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|15814993|gb|BI787268.1|BI787268
EST:     TATCAATTCATATAGCTTCTGATTATCTACTTGAGGAAGCTACAAATTTG                         TGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT
genomic: TATCAATTCATATAGCTTCTGATTATCTACTTGAGGAAGCTACAAATTTGgtaaatctcc ... attattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT
EST: gi|15815000|gb|BI787275.1|BI787275
EST:     TATCAATTCATATAGCTTCTGATTATCTACTTGAGGAAGCTACAAATTTG                         TGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT
genomic: TATCAATTCATATAGCTTCTGATTATCTACTTGAGGAAGCTACAAATTTGgtaaatctcc ... attattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT
EST: gi|6914968|gb|AW396498.1|AW396498
EST:     TATCAATTCATATAGCTTCTGATTATCTACTTGAGGAAGCTACAAATTTG                         TGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT
genomic: TATCAATTCATATAGCTTCTGATTATCTACTTGAGGAAGCTACAAATTTGgtaaatctcc ... attattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT
EST: gi|57575810|gb|CX548781.1|CX548781
EST:     TATCAATTCATATAGCTTCTGATAATCTACTTGAGGAAGCTACAAATTTG                         TGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT
genomic: TATCAATTCATATAGCTTCTGATTATCTACTTGAGGAAGCTACAAATTTGgtaaatctcc ... attattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagaaaaatatatttcaatatctaatttctttctttcctttttattattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGATCGTGTCAGAAATTTGTATTTCACTTTTCTCTTTGTTCTGCGAGCAGTAA
                     atctaat  putative branch site (score: 3)
                      tctaatttctttcttt  CT-rich tract
     aaaaatatatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatactggcacacccatgttactctaatacatttcactatgaacttgagaaaaatatatttcaatatctaatttctttctttcctttttattattccagTGGGGACAAAATCTTACTTTGATGTATGACCGAGTCCTAAGATACCCTGATCGTGTCAGAAATTTGTATTTCACTTTTCTCTTTGTTCTGCGAGCAGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
gcatact
- - - - gcacacc
- - - - - - - -catgtta
- - - - - - - - - - - - - - - - - - - tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - aaaaata