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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaactcatttaatatacgtttttttgtcaatatctactctcaatatgaaagacgtcaatctcttgctaaatatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC

Basic information

species Glycine max
transcript GLYMA17G37820.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 7
ataaaactcatttaatatacgtttttttgtc-aatatctactctcaatatgaaagacgtcaatctcttgctaaatatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC-
||    ||   |       |   ||| |||  |||| || || |  | |    | ||    |    |  || | |||  || ||||  |  |  | |  ||||| ||||||||||  |||||||| || || || ||||| || ||  | ||||||| ||| |||||||||||||| || || |||||||| ||||| ||  
attttgctgcatagtctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaa-taacttactatc-ttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 7
ataaaactcatttaatatacgtttttttgtca-atatctactctcaatatgaaagacgtcaatctcttgcta--aatatgatttaac---aactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC-
       |        | |  || |  ||  | | ||||  | |  | |    |   ||  |||| ||| |   |  |   |||||    ||||   ||||    |||| ||||| ||||  |||||||| || || ||||||||||||||| | ||| ||| ||| ||||||||||| || || || |||||||| |||||  |  
-------ttgggctggacatattatactgaaacacatctcttatatagaccttatttgtgcatctgttgttgttacaagtgtttaattcgaactcacttttatgtagGATTTGGTTAAGAAGTACTCTGAGTTCATCAACTTCCCTATCTATTTGTGGTCAACCAAGGAGGTTGATGTTGAAGTGCCAGCTGATGAGGATGAGACAA

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G141931_T01 (Zea mays), 3'ss of exon 7
ataaaactcatttaatatacgtttttttgtcaatatctactctcaatatgaaagac-gtcaatctcttgctaaatatgatttaac--aactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC-
      ||  |  |   | | | | ||    | | | ||     | | |    |   ||  |||| ||| || |  ||  | |    |  | | ||||   ||||| ||||||||||  |||||||| || || ||||||||||||||| | ||| | | ||| ||||||||||| || || ||  ||||||| |||||  |  
----gtctgctccaccctgcatctcttgtagactttataagacaagtctatttgtttgtgcatctgttgttacaagtgtctaatttgatttctcttttatgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAACTTCCCTATCTATTTGTGGTCGACCAAGGAGGTTGATGTTGAAGTGCCAACTGATGAGGATGAGACAA

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 7
ataaaactcatttaatatacgtttttttgtcaatat-ctactc--tcaatatgaaagacgtcaatctcttgctaaatatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC-
    || |  || |  ||   || |    ||| |   || ||   |||||||    |       |||| |  |   |   | | | ||    | | |   ||||||||||||||||||||| |||||||| ||||||||||||||||   | ||||| ||||||||||||||    ||||| || | ||| |||||||| ||  
---gaagtggttcagcat-tattatgaattcagtgcactgcttattcaatatttctgtttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 7
ataaaactcatttaatatacgtttttttgtcaatatctactctca-atatgaaagacgtcaatctcttgctaaa---tatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC-
     | | | ||  |     || ||||  ||||   ||       ||      || || ||| ||| | | |    | | ||||  | ||  |  |  |   |||| || ||||| ||||| |||||||| || ||||| || || ||  | ||||||||||||||||||||||| ||||| || || ||||||||||| ||  
-----agttaatttttgctttttatttttccaatgaatatgggagcattcttgtgatgtaaatatctggtttaggtttttaattttgctaccttgataattgtagGAGTTAGTGAAAAGATATTCTGAATTCATCAACTTTCCCATATACCTCTGGGCAAGCAAAGAGGTTGATGTAGAGGTACCTGCAGATGAAGATGAGTCAA

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|58017096|gb|CX703838.1|CX703838
EST:     CTTGCAGGAGTCTAAACTGAA                         AGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATTTATATTTG
genomic: CTTGCAGGAGTCTAAACTGAAagtatgcacc ... ttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTG
EST: gi|208107731|gb|GD902005.1|GD902005
EST:     TTACACCTCAAGGAAGAGGCTGGGGAGTACTTGCAGGAGTCTAAACTGAA                         AGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTG
genomic: TTACACCTCAAGGAAGAGGCTGGGGAGTACTTGCAGGAGTCTAAACTGAAagtatgcacc ... ttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTG
EST: gi|24205491|gb|BU964744.1|BU964744
EST:     TTACACCTCAAGGAAGAGGCTGGGGAGTACTTGCAGGAGTCTAAACTGAA                         AGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTG
genomic: TTACACCTCAAGGAAGAGGCTGGGGAGTACTTGCAGGAGTCTAAACTGAAagtatgcacc ... ttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTG
EST: gi|193638352|gb|FK586720.1|FK586720
EST:     AGGCTGGGGAGTACTTGCAGGAGTCTAAACTGAA                         AGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTG
genomic: AGGCTGGGGAGTACTTGCAGGAGTCTAAACTGAAagtatgcacc ... ttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgaaagacgtcaatctcttgctaaatatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC
                                         ctatttttttc  CT-rich tract
                        taaatatgatttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaactcatttaatatacgtttttttgtcaatatctactctcaatatgaaagacgtcaatctcttgctaaatatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - -gaaagac