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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

Basic information

species Glycine max
transcript GLYMA16G01830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
-----tcaggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA
         || | ||   |  |   ||  | |  ||    ||   | |    || ||  |    | | |   ||  || ||  | | |   || |      ||| | |||||  | ||||||||||||||||| |||||||||||||| || ||||| ||||| || |||||||||||||||||||||||  | |||||||| |
cttgacatagtgagaacagagaaaactgcat-tggattcaattgtagaaga--aagattttcctccctattgccactgccta-ctaactgaattttaattg-cagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA

upper sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 3'ss of exon 1
-----tcaggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA
     ||   ||  |  ||  | |    ||| |  |||   |     |||    |     |  ||    |   ||   |||||| || ||  |  | |   |||| | |||||  ||||||| || |||||||| ||||| || ||||| || ||||| || || ||||| | ||||||||||||||||||  | |||||||| |
actattctctttgcattttcgt-tagcatttctctatagcatcggatgatacctaccgtgtccaatgatttccca---cttaatcgaata-atcttatgtttcagATCACATACCACTTTTTCCATTGGAAGAAGGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAGCAAATGGACAATGGCA

upper sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
----tcaggttataaattaatattttgtttgt-aaatatt-gttaatggatgttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA
      |  | || |  |  | |  | | ||| ||| ||| ||  |||||   |     || | |   |  | |  |||  |       |   |  | |   |||| | |||||  ||||||| || |||||||||||||| || ||||| || ||||| || || ||||| | ||||||||||||||| ||  | |||||||| |
gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatg------tgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA

upper sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
tcaggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataa-tttaacttctctaca-tggcttaattgattatg--ttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA
|  ||||     || |  |||  | |   | | |  | ||    | |  ||  || |||  |      ||| | ||    | || | ||  |  | |   |||| | |||||  ||||||| || |||||||||||||| || ||||| || ||||| || || |||||   ||||||||||||||||||  | || ||||| |
tttggtttc---ttgaattttcatgtacta-tctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA

upper sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01230.1 (Arabidopsis thaliana), 3'ss of exon 1
----tcaggttataaattaatattttgtttgtaaatattgttaatggatgtt-aaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA
       | ||     | || |     |||      |||  ||||   | || |  | ||| | |  |||    |    ||  | ||| || ||||     ||||||||| ||| ||   || ||||||| |||||||||||| |||||||| |||||||| ||||||||| | || ||||||||||| ||  | ||||||||  
tggcattgcttgattgtcaaaaccaaatttaatctaatttctaattactctttaggaaaatgtgatgtctgagtagaaatttgtggat-at-ttgt---tgtcagGTAACGTATCACAGCTTCCACTGGATGAAAGGAACTCCTTTTGCAGATGACCAAGGAATCTACAATGGTTTAACTTGGTGGGAACAAATGGACAATGGTC

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|31459292|gb|CD401320.1|CD401320
EST:     CCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: CCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|254346297|gb|GR859910.1|GR859910
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|298185731|gb|HO030944.1|HO030944
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|254348679|gb|GR852358.1|GR852358
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAGAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|16348288|gb|BI973883.1|BI973883
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|151412762|gb|EV282574.1|EV282574
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|5606135|gb|AI900233.1|AI900233
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|254346298|gb|GR859911.1|GR859911
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|16996257|gb|BM085629.1|BM085629
EST:     GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
EST: gi|21601782|gb|BQ612113.1|BQ612113
EST:     GCTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCT                         GTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC
genomic: GTTGTTCTCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatccctct ... tgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA
     aataatttaacttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - tggatgt
- - - - - - - - - - - - - - - - - - - - - - - - aaaataa