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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactgcccgtcggccatccccatacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG

Basic information

species Glycine max
transcript GLYMA04G03030.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------tcactgcccgtcggccatccccatacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
                                                    | |     | |      |     | |  | | |  |   | | || | ||  |  | | ||         ||       | ||| |||  | || ||||||||||| |||| ||||||||||| || || ||| ||||||| ||| ||||  | || || |||||  | ||||| |||||||||||||||||||||   |
gtatattcttgatttatttggcgtctctatttttaagtgaaaaaaacattggttaagatactttatttgtggtgttcctatgaacaacaaatattttattcatta-ctctcaatggttgctttgtgattgtttgtg-cttcgttttatgcagCAATTCCTGAAGGAGATTCTGAATGATCTGTGTTTTTACAACAAACGAGGACCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCTACAG

upper sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g56550.3 (Oryza sativa), 3'ss of exon 5
--------------------------tcactgcccgtcggccatcccc----atacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
                             | |   || |  |||        | |     ||| ||   | |  ||        || | | |  | | ||| ||    |||  | ||| ||  | |||||||||||||||| |||||  |||| || || ||| | ||||| ||||| ||| | |||||||| ||  | || || |||||||| ||||||||||||   |
gtattttttctcaagttatcctaattatgccgagggtggagcatttgttaagaaattgctagcaccaactctagttattgcatgttctgatatcaaagcctcaact--ctcccggcttgtttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGTCCAAATCAAGGGACGCATGAACTTAAGCCTGAATACAAGAAATCTACAG

upper sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G060284_T01 (Zea mays), 3'ss of exon 5
-----tcactgcccgtcggccatccccatacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
     ||  || || |   |         |  |  |      ||| | |||         || |   |  | || ||     | |  | |  |||   | ||||||||||| |||| |||||  ||||||| || ||||| || |||||| ||||| | || || |||||  | ||||| ||||||||||||||||||||    |
gtatttccttgtccctttcctgaagtgtgatgcatattattatttatgtttcctctattgttctctgactgctcgtgtggttattatttatgtttctctatgcagCAATTCCTGAAGGAGATATTGAACGATCTGTGTGTGTATAATAAACGAGGTCCAAACCAGGGAACGCATGAGCTCAAGCCTGAGTACAAGAAATCCACAG

upper sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 5
--tcactgcccgtcggccatccc-catacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
  |   |||  |     ||      |   ||   |    ||  |  | ||  |     | || |    | ||  ||||    | |    || ||  |||||||||||| ||||||||||| |||||||| || || || ||||||||||||||  ||||||||||||| || ||||| ||||| || || |||||||||| ||
tctttttgcttgcttatcacaaaataattacatggtgtactagtattctttgattggatcttcacct-ggtcaggaatt--ttgggtgtttctttctttgcagCAATTTTTGAAAGAGATACTGAACGAGCTCTGCGTGTACAATAAAAGAGGAACCAATCAAGGAACTTATGAGCTTAAGCCAGAATATAAGAAATCTGCTG

upper sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S149_261V6.1 (Physcomitrella patens), 3'ss of exon 5
tcactgcccgtcggccatccccatacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttt---tgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
   | |   |      |     ||  | |        |   |     |  |         | ||  || |   ||||  | |||    ||    |   |||||   ||  ||||||| || ||||| || || ||  | ||||| |||||||| || |||||||| || || ||||||||||| |||||||||    | |   
--gcggtggggaaaggaggtggatg-atttgttggtatgggtgggaagtgggtgacacagagaagcatgcaagatgagttggtggtggttgtggtgtgtgcagGCGTTTCTGAAAGAAATACTGAATGACCTGTGCATCTACAACAAAAGAGGCGCGAATCAAGGGACGTATGAGCTGAAGCCAGAGTACAAGCGGACCGAGA

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|13789420|gb|BG652011.1|BG652011
EST:     AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgctttt ... tcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|193494557|gb|FK459759.1|FK459759
EST:     CCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: CCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgctttt ... tcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|192308909|gb|FK002133.1|FK002133
EST:     AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgctttt ... tcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|193417373|gb|FK383849.1|FK383849
EST:     GCCTAATTGGGTCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: GCCTAATTGGG-CCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgctttt ... tcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|10252793|gb|BE820559.1|BE820559
EST:     AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgctttt ... tcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|208101107|gb|GD900538.1|GD900538
EST:     AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgctttt ... tcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
EST: gi|15814595|gb|BI786870.1|BI786870
EST:     AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCA                         CAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT
genomic: AGCCTAATTGGGCCTTGAAACAGCTTGTCCAAGAGACTGATCAACCTGCAgtatgctttt ... tcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG
                                        ctttttcttttgc  CT-rich tract
       aatttttaaaaaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcactgcccgtcggccatccccatacactcagccccctttttcttttgcagcaatttttaaaaaagatcctgaatgaactcgtgactttttcttttgcagCAATTCTTGAAAGAGATTCTGAACGAACTTTGTGTTTACAATAAAAGAGGTGCCAATCAAGGAACCTACGAGCTGAAGCCTGAGTACAAGAAATCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
-cactgcc
- - - - - - - -catcccc
- - - - - - - - - - - -tacactc
- - - - - - - - - - - - - - - - ccccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactt