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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttgcatgtgatcttggaaccctgtcatggtagggcattttaaagttccttaatcaaactcatcatgactttcatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGG

Basic information

species Glycine max
transcript GLYMA10G07820.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 3'ss of exon 8
gtatg-gttgcatgtgatcttggaaccctgtcatggtagggcattttaaagttccttaatcaaactcatcatgactttcatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGG
|||||     | |   |      ||        | |     || | | ||      | |       | |     |  |   | ||     |||| | || ||| || || ||| ||||||| || || ||||||||||||||||||||||||||||| || || || |  ||     |  | ||||| || |
gtatgtacatcttccaaatccaaaatagctctgtagctct-cagtgtgaatgcaaatgactgtctgctttccatcggttccctatttactagGTCACAGCAGTTAACCTGAAGAATGGCAGTGTGCTTGAAGCTGATATTGTTGTTGTTGGTGTTGGGGGCAGACCGCTGACTACTCTCTTTAAAGGTCAAG

upper sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G084881_T01 (Zea mays), 3'ss of exon 7
gtatggttgcatgtgatcttggaaccctgtcatggtagggcatttta----aagttccttaatcaaactcatcatgactttcatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGG
    |  || |      |    | ||| ||   | |      || ||     || |||  |     |||     | | ||   ||   | | ||||| |  | ||| || |||||||||||||  || || ||||| |||||||||||||| ||||||||||| || ||    ||     |  |||| || || |
----gtatgtaaaaccccccaaagcccagtttagctgtaaatttctatctgtagatccaaaggtttacttgatttaatttgtttcttgcttacagGTCACTGCAGTTAAGCTAAAGGATGGCACAGTACTTGAAGCCGATATTGTTGTTGTCGGTGTTGGAGGCAGACCATTGACTACTCTCTTCAAGGGTCAAG

upper sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 7
gtatggttgcatgtgatcttggaaccctgtcatggtagggcattttaaagttccttaatcaaactcatcatgactttcatcc-atcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGG
   |  || | ||      ||  |   |   ||  |||    | ||   |  |   |  |       |    | ||   ||  |||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||||||||||||||| ||||| || |  |||   ||| ||||||| ||||
--gtaatttcttggacatctgatatgtta--attttagtatttatttgggagcaaaagccttttatgtagcaatttgagtcttatcattcagGTAAAGGAAGTGAAACTTAAGGATGGTAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGG

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|193493627|gb|FK458809.1|FK458809
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAA
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAA
EST: gi|192330173|gb|FK019798.1|FK019798
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|193551352|gb|FK507591.1|FK507591
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGA
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGA
EST: gi|151411030|gb|EV280841.1|EV280841
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|21255678|gb|BQ452566.1|BQ452566
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAATATAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAA-AGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGT
EST: gi|192295928|gb|FG992679.1|FG992679
EST:     GTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: GTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|21677236|gb|BQ629587.1|BQ629587
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|192295927|gb|FG992678.1|FG992678
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|254331131|gb|GR843250.1|GR843250
EST:     GTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: GTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|6913394|gb|AW394924.1|AW394924
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|254344724|gb|GR851314.1|GR851314
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|254340648|gb|GR854376.1|GR854376
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTA-TTCTGATGGAGAG                         GTAAAAGA-GTCAAACTAAAGG
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGG
EST: gi|9204276|gb|BE330500.1|BE330500
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggcattttaaagttccttaatcaaactcatcatgactttcatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGG
                ccttaat  putative branch site (score: 4)
                                     ctttcatcc  putative PPT
     attttaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttgcatgtgatcttggaaccctgtcatggtagggcattttaaagttccttaatcaaactcatcatgactttcatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA