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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggtttaaattcacccgtttgatggtaatttagttgtgcctaggtacagtgttttctaatttatgaatttttatatgaacaatatccttgtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACA

Basic information

species Glycine max
transcript GLYMA18G16160.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G16160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 3
-aaggtttaaattcacccgtttgatggtaatttagttgtgcctaggtacagtgttttctaatttatgaatttttatatgaacaatatccttgtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACA
     |||  ||| |   |  |  || |  | ||  |||  | |  |  | | ||||  |  |||   | | | | || |    ||        |   |||||||||| ||| |||||||||||||||| || ||||||||||| || |||||||| ||||| ||||||||||| ||||||||||||||||
tcctttttgtatttattggcattttgttcttgtacgtgtcaccaattgtactcttttacatgtta-acactgtcaaattatgtttacttcgccatcgccagGTACGTTCAAGCTGACACTTCAGTTTACTGAAGATTATCCTAACAAGCCACCTACAGTGCGATTTGTTTCTCGGATGTTTCATCCTAACA

upper sequence: GLYMA18G16160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T04 (Zea mays), 3'ss of exon 3
--aaggtttaaattcacccgtttgatggtaatttagttgtgcctaggtacagtgttttctaatttatgaatttttatatgaacaatatccttgtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACA
  |    ||| ||||    ||     | |  | |   || || ||  ||||  |||| ||  | |        | |||||   | |    || | || ||||||||||||||| |||| || |||||||  || || ||||| || |||||||| |||||||| ||||||||| | ||||| ||||||||||
acagctcttagattc-tgtgtcactagcttgtctttctgagcttac-tacatggtttgcttctgtcctttgactgatatgctaactcctgttttattctcagGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA

upper sequence: GLYMA18G16160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 4
aaggtttaaattcacccgtttgatggtaatttagttgtgcctaggtacagtgtt-ttctaatttatgaatttttatatgaacaatatccttgtc----ttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACA
     |  ||||     ||||||||    ||| || ||    |||     | |  || |  ||  ||  | ||||      | ||   ||  |       ||||||||||||||| ||||| ||||||||||||||||||||||| ||||| ||||| ||||| || ||||||||| ||||||| ||||| || |
-----tacaattgttttgtttgatgtatttttcgtggttatgagggcacttatgattattgttggtgtgtatttaatgctgctatgctctgattgaatccttcagGTACGTTTAAATTGACGCTTCAGTTTACAGAGGATTATCCGAATAAGCCACCAACTGTACGCTTTGTTTCTAGAATGTTCCATCCAAATA

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|208327169|gb|GE118485.1|GE118485
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|209728174|gb|BW651609.1|BW651609
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|9986725|gb|BE660833.1|BE660833
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACCGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCA
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTAC-GTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCA
EST: gi|22926835|gb|BU543974.1|BU543974
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|193570531|gb|FK524958.1|FK524958
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|13311395|gb|BG405046.1|BG405046
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|21255605|gb|BQ452493.1|BQ452493
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTATTTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|13480716|gb|BG510059.1|BG510059
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|254333697|gb|GR848615.1|GR848615
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|17518903|gb|BM187945.1|BM187945
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|192294426|gb|FG987355.1|FG987355
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|4292045|gb|AI437706.1|AI437706
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|254333698|gb|GR848616.1|GR848616
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|192305566|gb|FG998322.1|FG998322
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|26269575|gb|CA820638.1|CA820638
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACTTTTAAGTTGACACTTCAATTTACACAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|254320629|gb|GR827078.1|GR827078
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|193369402|gb|FK336664.1|FK336664
EST:     CCCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|15812366|gb|BI784641.1|BI784641
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|22926846|gb|BU543985.1|BU543985
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|4295885|gb|AI442396.1|AI442396
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
EST: gi|192296666|gb|FG991234.1|FG991234
EST:     ACCAGATGACACCCCTTGGGATGGAG                         GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC
genomic: ACCAGATGACACCCCTTGGGATGGAGgtacaattat ... gtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagtgttttctaatttatgaatttttatatgaacaatatccttgtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACA
         ttctaat  putative branch site (score: 2)
                                      tatccttgtcttttc  putative PPT
     tgttttctaatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggtttaaattcacccgtttgatggtaatttagttgtgcctaggtacagtgttttctaatttatgaatttttatatgaacaatatccttgtcttttcagGTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACA

- - - - - ttcaccc
- - - - - - - - - - -gatggta
- - - - - - - - - - - - - - - - - ttgtgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaac