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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttcatgctagacattggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

Basic information

species Glycine max
transcript GLYMA16G01810.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 9
------------------------------gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttcatgctagacattggttttctgatagatacct-tttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
                              | ||| ||  | |||||  |   | || |  |    | || | |    | |  | ||||||  | |||   |||| | | |  ||| |||| ||| | |||||||||||||||||||||| ||||||||||| || |||||||| || || |||||  |||| || || || ||||| |||||||||||||| ||||| ||
gtaactggaagaactttgaaacttcgttctgggtggtttcttctagatttgtttgttatagtctccacctcaaaa---gcggataatgctaagctttg---ttctcacaaactcctgtttgctgt-tacagGAGCTGATATAAGGAGTGTCTGCACAGAAGCTGGCATGTATGCGATTCGCGCCCGACGGAAAACAGTGACTGAGAAGGACTTCCTTGATGCTGTAAACAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 9
----------gtgtgcttcatgctagacattggt-tttctgatacat--atctgaca---ttgtgtgcttcatgctagacatt--ggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
           |||| ||   ||   |  || || |||||| |  ||  |  |||     |||    |||   | ||||   |  |||| ||  ||||      ||||||  |||||||||| ||||||||||| || |||||||||||||| |||||||| || |||||||| ||||| || || |||||||| || || || ||||| || |||||
gtgagttgctttgtggtttcagcagaatgtttgtgtttctgcttgattcaattgatttacttgaagactttgcgatagatgatcaggttctcacatagccttgctttgtta-ctccagGAGCGGATATAAGGAGCGTCTGCACAGAAGCCGGGATGTATGCCATTCGTGCCCGCAGGAAAACGGTGACAGAGAAGGATTTTCTCGATGCTGTCAATAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 8
gtgtgcttcatgctagacattggttt-tctgatacatatctgacattgtgtgcttcatgctagacattggttttctgatagatacctt--ttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
                   | | ||  |||||    | ||||      | |  |  |||  ||||  |    |||| | |  | ||||  |||||| |||||||||||||||||||||| || |||||||||||||| ||||| || || || ||||| ||||| || || ||||| || || || || ||||| || || ||
----------------gtgtggtttcatctgagtggtttctgc-----tttattcgatgacagacgatcaggttctcacat-tgccttgcttgttg-ctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCGCCCGCAGGAAAACGGTGACAGAAAAGGATTTTCTCGATGCTGTCAACAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
---gtgtgctt-catgctagacat-tggttttctgatacatatc--tgacattgtgtgct-tcatgctagacattggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
      | |||   ||   | ||  | || ||   ||||    |  |||   | |  ||| | ||  | |    | | ||| |   | ||  |||||      | ||||||| || ||||| ||||| ||||| ||||| || ||||||||||| || || || |||||||| || || ||||| |||||||||||| |||| || ||
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatat-tctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttca-tgctagacattggttt-tctgatagataccttttgttg-tctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
|  || | || ||  |||  | |  |  ||    ||   |||  |  |  ||   | ||  | |  |       | | |  ||  |   |  ||| ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||
gaatgatgcaggc--gactgtagaatgttgtcgaat-cgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttc-atgctagacattgg--ttttctgatagataccttttgttgtc-tccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
   ||   ||| ||  | |   |  |  ||    || | |||  || ||     |  |   | || ||    |  |  |   ||  |    ||||    | |||| || |||||  ||||||| || || || || ||||||||||| || ||||| || ||||||||||| ||||||||||||||| | || || || |||||
---tggaacattctgtaaagccgagtgttgtagtat-tttgagcttatgaatacctgtataaaactttaaaatcatgcgcctgaaccaagctgttcctgttcagGTGCGGATATTCGGAGTGTGTGTACGGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAAGACTTCTTGGAAGCTGTCAATAA

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
-gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttcatgctagacattggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA------
 |   ||  | ||    |  |||       |  |  |      || |  |||    ||   | ||  ||    |     |  | | |       ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||      
tgcaggcgac-tgtagaatgttgtcgaatcgtgagttgatcagcacta-gtgtgaaatctcaaaccatgtcactgaagcaagtgcttg-----atctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT

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|254320082|gb|GR830998.1|GR830998
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|207710520|gb|GD690756.1|GD690756
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|214005791|gb|DB988688.1|DB988688
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|26269017|gb|CA820080.1|CA820080
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAATGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|6847793|gb|AW350083.1|AW350083
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|4437003|gb|AI522868.1|AI522868
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|208149915|gb|GD944223.1|GD944223
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|8827828|gb|BE211558.1|BE211558
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCATG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|18039872|gb|BM308166.1|BM308166
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACA
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACA
EST: gi|26269018|gb|CA820081.1|CA820081
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|214007684|gb|DB986050.1|DB986050
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|19268833|gb|BM885089.1|BM885089
EST:     AAGGGATATTCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|18715759|gb|BM522851.1|BM522851
EST:     GGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: GGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|7327123|gb|AW620985.1|AW620985
EST:     TTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: TTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|298174191|gb|HO017527.1|HO017527
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAGATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|208156494|gb|GD956818.1|GD956818
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|33390699|gb|CA853894.1|CA853894
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|254319816|gb|GR829220.1|GR829220
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|193648414|gb|FK597105.1|FK597105
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|8286217|gb|BE023776.1|BE023776
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|298171740|gb|HO021332.1|HO021332
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
EST: gi|209717051|gb|BW668705.1|BW668705
EST:     AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTG                         GAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG
genomic: AAGGGATATCCGATTTGAACTTCTGGCTCGGCTTTGCCCAAATTCCACTGgtacggacat ... ttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgcttcatgctagacattggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA
                          ttctgat  putative branch site (score: 3)
                                      ccttttgttgtctcc  putative PPT
                               atagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttcatgctagacattggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
gtgtgct
- - - -tcatgct
- - - - - - - - - - - - - -ctgatac
- - - - - - - - - - - - - - - - - - -tctgaca
- - - - - - - - - - - - - - - - - - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatag