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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctgatcttgttttgttcatcacatagttatttttctgttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

Basic information

species Glycine max
transcript GLYMA10G42940.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 12
gtctctgatcttgttttgttcatcacatagttatttttctgttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
      |  | | || ||     || |   ||  ||||| |  ||| |  |  |  ||     ||| |  |    | | || | ||||||| || || || |||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||| || |||||||| |||
------gtacctattatgagt-ccataggctttgttttcaga-catgatgtgtaagatga---attgacatctactgttttctgttcagCTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
-------------gtctctgatcttgtt--ttgttcatcacatagttatttttctgttcatcacatagactatat----ctcattcatgt-tatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
             |||  || | || ||  |     |   ||||||   ||| ||   | ||| | |   | |         ||| |  | |  | || | | |||||||| || || || || || || ||||||||||| ||||| ||||| ||||| |||||||| || ||||| || |||||||| |||
gtacatactatgagtccatgttatttttgataagggagtccatagtc--tttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------gtctctgatcttgttttgttcatcacatagttatttttctg-ttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
                               |  | ||    | |||||| ||   |   ||| || ||   ||  | |    ||   || ||  || ||  | ||||| |  ||| ||| | || || ||||| ||||| |||||||| |||||||| |||||||| ||||||||||||||||| ||||| || ||||| |||
gtaagactttatttcttgtccattaccagcattgcagaaaa-gctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgtt-attatgtttttgtgattt-cagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
gtctctgatcttgttttgttcatcacatagttatttttctgttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
     |  | || |  |||||         | |  ||    || | ||| |         |  | | |||  ||| ||  || ||||||||||| ||||||||||| || || |||||||| || ||||||||||| ||||||||||||||||||||||| |||||||| |||
----gtagtatt-tgatgttcgggctgcgttcaccttctctttgagcacgt--------cccaactaatgcgattctt-cttctttcagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 12
-gtctctgatcttgttttgt--tcatca-catagttatttttctgttca---tcacatagactatatctca----ttcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
    |  || | |  |||||   ||||| | |    ||||||||| | |      | |     |   ||      || |  |  | | ||    || ||| | |||||||| ||||| || ||||||||||| || || ||||| || ||||| |||||||||||  | || || ||||| |||
cacatgagagcatcatttgtggccatcaacttccccatttttctgatgaagtctgcttgagtcaagactttgggtttaacatggtgtctacccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------gtctctgatcttgttttgttcatcac--atagttatttttctgttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
               |  || |  || |  ||||||      ||| |||  | | ||  ||      ||  |  || | |  || ||  ||   |||  || ||| | |||||||||||||||||||| ||||||||||| || ||||| || ||||| ||||| |||||  | || || || || |||
tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtga-caatggggagtttggatttga--caagtcgtt--gattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG

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|19452473|gb|BM953883.1|BM953883
EST:     CTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG                         CTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATG
genomic: CTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATG
EST: gi|15813509|gb|BI785784.1|BI785784
EST:     CTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG                         CTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
EST: gi|16283344|gb|BI945501.1|BI945501
EST:     TATTGGTGAGGGAATGACTAGAAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
genomic: TATTGGTGAGGGAATGACTAGAAA-GGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
EST: gi|16283207|gb|BI945427.1|BI945427
EST:     CTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG                         CTCTACGCAGATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
EST: gi|16279679|gb|BI943560.1|BI943560
EST:     CTATTGGTGAAGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG                         CTCTACGCAAATTATGCTATCGGAAAGGATGTGCAAGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
EST: gi|7686714|gb|AW757362.1|AW757362
EST:     GTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG                         CTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG
genomic: GTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
                                    ttatttttattttttt  CT-rich tract
                     tatatctcattcatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctgatcttgttttgttcatcacatagttatttttctgttcatcacatagactatatctcattcatgttatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC