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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttataggatccaattcctttttgataacctcatttttgtatccttgatggcatggaaattcaagaatcctagatcttaatgtctgtcattggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAAGCGGGACAAACCATGTCCTTCCTACTTATGGCTATGCAAGAATGTATGG

Basic information

species Glycine max
transcript GLYMA15G13910.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 12
ttataggatccaattcctttttgataacctcatttttgtatccttgatggcatggaaattcaagaatcctagatcttaatgtctgtcattggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAAGCGGGACAAACCATGTCCTTCCTACTTATGGCTATGCAAGAATGTATGG
 ||||||        | |   ||  | | || |  |  |  |||  |     |   | |||||   |     |||| |     |    ||  |    |||| || || || || || |  ||||| || ||||| || || || ||||||||||| ||||||||||||||||| || ||||| || ||||| |||||| |
gtatagg--------catacctgtcagcgtcttaatcttgacctgaacattttcatacttcaatggt----aatctcaggcgatcgttttttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAAGCGGCACAAACCATGTCCTTCCAACCTATGGTTACGCAAGGATGTATAG

upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 14
------------ttataggatccaattcctttttgataacctcatttttgtatccttgatgg-----catggaaattcaa----gaatcctagatcttaatgtctgtcattggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAAGCGGGACAAACCATGTCCTTCCTACTTATGGCTATGCAAGAATGTATGG
            || | |     |  |    | || | || |  || ||  | |   |||||     | |||    ||||    |||| || ||||  ||| | ||   |     |  |||| || || || || || |  ||||| || ||||| || || |||||||| |||||||| |||||||||||||| || ||||| || ||||| |||||  |
gtaggcatattttttttgtcattagctttggtgtggtcacattgttcttcaagca--gatggttccccttggggcatcaatcttgaattcttgatcgaaatatttggtttctttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGAGCGGGACGAACCATGTCCTTCCGACCTATGGTTACGCAAGGATGTACAG

upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 14
---ttataggatccaatt--cctttttgataacctcatttttgtatccttgatggcatggaaattcaagaatcctagatcttaatgtctgtcattggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAAGCGGGACAAACCATGTCCTTCCTACTTATGGCTATGCAAGAATGTATGG
   |||    |  |||    || |   |   |    ||   | | |   | |     |||   ||  | |||||    || ||   | |     |  ||||||||||||||||||||||||||  |||||||| || ||||| || ||||||||||| || ||||||||||||||||| || |||||||||||| | ||||||||
tgattaagaaaaacaagagaccatgcagcccagtcaataactatgtttatcac----tggtgtttttataatccagcctcatatcatttacttctc-ctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG

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|15203715|gb|BI426483.1|BI426483
EST:     TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         GTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAA
genomic: TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAA
EST: gi|31311594|gb|CD396797.1|CD396797
EST:     AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|31311594|gb|CD396797.1|CD396797
EST:     AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|31311594|gb|CD396797.1|CD396797
EST:     AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|31311594|gb|CD396797.1|CD396797
EST:     AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|31311594|gb|CD396797.1|CD396797
EST:     AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: AATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|254340469|gb|GR850771.1|GR850771
EST:     TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|254340469|gb|GR850771.1|GR850771
EST:     TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|254340469|gb|GR850771.1|GR850771
EST:     TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|254340469|gb|GR850771.1|GR850771
EST:     TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-
EST: gi|254340469|gb|GR850771.1|GR850771
EST:     TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAAT                         G
genomic: TAATTATCAATGTGAAAGATGCAGAGAAGTGGGAGAGTTTCATTGAGAATgcaggtgctc ... ggctctgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggcatggaaattcaagaatcctagatcttaatgtctgtcattggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAAGCGGGACAAACCATGTCCTTCCTACTTATGGCTATGCAAGAATGTATGG
                            tcttaat  putative branch site (score: 3)
          aaattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttataggatccaattcctttttgataacctcatttttgtatccttgatggcatggaaattcaagaatcctagatcttaatgtctgtcattggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAAGCGGGACAAACCATGTCCTTCCTACTTATGGCTATGCAAGAATGTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - caattcc
- - - - - - - - - - - - - - - - - - - - - - - - -gcatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtca