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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaactcttgaaactgttcccatgtaaaagtaactcaactcttaaagagaggattgatgcaccttttcgcttttaaaaacatttttgtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA

Basic information

species Glycine max
transcript GLYMA07G10000.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 7
---------------------------------ctaaactcttgaaactgttcccatgtaaaagtaactcaactcttaaagagaggattgatgcaccttttcgctt-ttaaaaacatt----------tttgtggtggt-tgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA
                                   |||   || ||| | ||    || || ||   ||  ||| || |   |   | |       |||  || || ||  |||| |           ||| |||   | || |||| |||||||| || |||||||| ||||||||||||||| |  | || || || |||||||||||  |||| ||||| ||||||||||| |||||||| |
gtcacaagcaaaatatcttcataaaattttacttgaaataattcaaattatttgtttgcaacag---ctttactgttcagttgtttactaccattgcttcacgattgttggaaacctgacttgctttgtttctggcattctgtagGAGGCTACAATCGAACAACTTCTTCCTATTTTCCTTTCTTTGCTCAAGGATGAATTTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
ctaaactcttgaaactgttcccatgtaaaagtaactcaactcttaaagagaggattgatgcaccttttcgct---tttaaaaacatttttgtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA
         ||| |    |   ||| |||  |   |    ||   || |  |  ||||      ||  |  |   | |||    ||  |        | |||||||||||| ||||| || ||| | || |||||||| ||| | ||||||||||| |||||||||||  | || || || |||||||| ||||||||||| |
--------gtgatatcagtg--atgcaaacatgtgtt---tccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 8
ctaaactcttgaaactgttcccatgtaaaa----gtaactcaactcttaaagagaggattgatgcaccttttcgcttttaaaaacattt-ttgtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA
      |    | | | || || ||  |       |      |    ||   |  || ||| |     |||    ||| |  || || | |  |  |   |  |||| || ||||| || ||||||||||| ||||||||||||||  | ||||| ||||||||||||||| | || |||||||||||||||||||||||||| |
-----tttggtagattttttccctgagatgttctatggagtgatctatatccactggtttggtctctgtttgtcatttaattaatatatatctttattcctatagGACGCAACAATAGATCAACTTCTGCCCATTTTCCTTTCTCTGCTTAAAGATGAGTTTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S117_137V6.1 (Physcomitrella patens), 3'ss of exon 6
ctaaactcttgaaac--tgttcccatgtaaaagtaac-tcaactcttaaagagaggattgatgcaccttttcgcttttaaaaacatttttgtggtgg---ttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA
   |||  |||| ||  |||   |   |    || || ||||  ||  |    |    |  |  |  ||| |     | ||  ||||  ||  ||     |  ||||| || || ||||||||||||||||| ||||| ||  |||| ||||| ||||||||||| |||||  | || ||||| ||||||||||| || ||||| |
--caacagttgatacggtgtgttctctttgtggtgacgtcaaagctctagactaaatgtcgtttaattttcca----tcaactcattcctggtgtcaatttcacagGAAGCCACCATTGAGCAACTTCTGCCCATTTTTCTAGCTCTCTTGAAGGACGAGTTTCCAGATGTACGACTTAATATCATCAGCAAGCTAGACCAAGTCA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 6
ctaaactcttgaaactgttcccatgtaaaagtaactcaactcttaaagagaggattgatgcaccttttcgcttttaaaaacattttt----gtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA
  ||||| ||| |    |     || |    |  || ||    |  | | ||  |      |    |  || ||| ||   || |||     |  |  |||||||| ||||| ||||||||||||||||| || || || || || ||||| || || ||||| |||||  | |||||||||||||||||||| ||||||||||
tcaaact-ttggattgatatttctgcatcctt--cttaatatctgcata-agcctctcaaaagtgatctgcatttcaatgtatcttttggcatcatttttgcagGAAGCTACCATTGAGCAACTTCTGCCCATATTTCTGTCACTGTTGAAGGATGAATTTCCAGATGTGCGACTAAATATTATCAGCAAGCTAGATCAAGTGA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 3'ss of exon 6
---ctaaactcttgaaactgttcccatgtaaaagtaactcaactcttaaagagaggattgatgcaccttttcgcttttaaaaacatttttgtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA
    || | | || ||| | || |||||   || | | |  |      |    | ||  ||  || | | |   |        | ||  | |  |   ||||||| ||||| |||||||||||| | || || ||||| || || ||||| || || ||||| || ||  |||||||||| ||||||||||| |||||||| |
gttttataatttttaaaat-tttccatgaccaactgagtatatatgctatccaatga--gagacaacgtgtaattccgtgttgctttggttttatctatgcagGAAGCTACTATTGAGCAACTTTTACCCATATTCCTATCACTGTTGAAGGATGAATTTCCAGACGTGCGGCTAAATATCATCAGCAAGCTAGATCAAGTCA

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|193520014|gb|FK474603.1|FK474603
EST:     CACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAG                         GATGCCACAATCGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
genomic: CACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAGgtaaatatca ... gtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
EST: gi|14258560|gb|BG881468.1|BG881468
EST:     GCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAG                         GATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
genomic: GCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAGgtaaatatca ... gtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
EST: gi|8285673|gb|BE023232.1|BE023232
EST:     GCTCTGCACTGGCTTCCGTTATAATGGGTATGGCACCAGTGTTAGGGAAG                         GATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
genomic: GCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAGgtaaatatca ... gtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
EST: gi|192310534|gb|FG999543.1|FG999543
EST:     GCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAG                         GATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
genomic: GCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAGgtaaatatca ... gtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGAC
EST: gi|207846884|gb|GD819103.1|GD819103
EST:     GCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAG                         GATGCTACAATTGAGCAACTTCTGCCTTATTTTTCCTTTCTCTTTTGAAAG
genomic: GCTCTGCACTGGCTTCTGTTATAATGGGTATGGCACCGGTGTTAGGGAAGgtaaatatca ... gtggttgcagGATGCTACAATTGAGCAACTTCTGCCT-ATTTT-CCTTTCTCTTTTGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagaggattgatgcaccttttcgcttttaaaaacatttttgtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA
       gattgat  putative branch site (score: 4)
                          ttttaaaaacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaactcttgaaactgttcccatgtaaaagtaactcaactcttaaagagaggattgatgcaccttttcgcttttaaaaacatttttgtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - ctgttcc
- - - - - - - - - - -catgtaa
- - - - - - - - - - - - - - - - - - caactct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtg