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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

Basic information

species Glycine max
transcript GLYMA07G15170.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
-------------------------------gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgtttta---cagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                |    |         ||   | ||| ||  | | |  | |   |  ||||  |   |  |     |    | |||  |  |   |||| | | |   |||||||||| || ||||| || || |||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| |||||||| || ||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtat-ctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtttgtaaagat-taaacttcatggaattataagtgtgcacaca-cacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
    ||||  || |   |||||   |     | ||    ||||| |  | |        | || |    |||         | |   ||||  ||| ||||||| || || ||||| |||||||||||||||||||| || ||||| || |||||||| || || || || |||||  ||||||| |||||||| || ||
----gtaactatgtttgcttcacacaggataaggttgttacacatcttattactggtctctattgtactaagttgtgaagttccctattattatttgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
    || |         || ||   | | | ||  | |  |      ||  |     |  |  |  |||   | |   ||| |  || | ||   ||||||| || || ||||| || || ||||| |||||||| |||||||| ||||| ||||||||  | || || ||||  ||||||||||| ||||| || ||
----gtcagtcgcctcttttattctacttttagcatcccaagctttgcttgatttcactgtaac--aaaatctcagatcttatgcttctatt--gcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
---gtttgtaaagattaaacttcatgga---attataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaa-tgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
    |         ||  ||||  || |   | | | ||| || | |   | |        || |||  ||||   |||   |||| | | |||||||     |||||||||||| ||||| || ||||||||||||||||| || ||||| || || ||||| || || || || |||||  ||||||| |||||||| || ||
gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgta-atttatagcatgtcaaggaat--ctgatgaagtgcctgccatttttttatgt-----agATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                 |   |||  || |  |    || |    ||  |  |  |    | | |  |    |      |  |  || |  |   |||||||||| || ||||| || || || ||||||||||||||||| ||||| || |||||||| || ||||| || |  || |||||||| ||||| || ||
----------------gtcagtggttttcttcggtgtcatattt-cagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
------gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
       |||||||   |||   ||  |     ||||  |||    |||||     | |   |      |||  | | ||      |  | |     ||  ||||||| || || ||| | || ||||||||||||||||| || ||||| || ||||| |||||||| || || |||||  | ||||| |||||||| || ||
gtagccatttgtaactcttatttttgctattgatatagttgta---acacatttctagattggt-----ctgtgacaata------ttccatcggaattggcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
           | |   |   ||| || ||   ||           || | ||  |    | ||   ||   |      | || ||    |  | |||||||||| || ||||| || || ||||| ||||| || ||||| || || ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
------gtcagtgattttctctggtatcatgcttgctt-------tacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgc-cttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
||||||| | | ||   |||         |||      | | | |  |||      ||||||||||    |   | |  || | |||| ||| |  ||||||| || |||||||| || ||| ||||||||||||| |||||||| || || ||||||||||||||||||||||| |||||||||||||||||||| ||
gtttgtatacactatctttc---------taa-----tatatagaagctg-----ggcaatggctggtctaaccaagtgctgcactttttgtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                   | | |   | ||     || ||    ||||    || | |  | |  | |   |      ||||  || |  | | |   |    |   || | |||||||||| || |||||||||||| ||||||||||||||||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaa-attc-cttttagtcgtttttaggcttgaatatgagtactcaccacatg-attctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------------gtttgtaaagatt--aaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctct-ttat-gttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                                             | |||  |  ||  | |||    ||||||       | |   | |||    |         ||  |   | |  | |||    | |   || ||| | ||||||| || |||||||||||||| ||||||||||||||||| ||||| || ||||||||| | || ||||| || ||  | ||||| || |||||||| ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggc-cacgtccatggtgatcttgcattcgataagactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 12
--gtttgtaaagattaaac--ttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
   ||| |  |   ||||   |   |||  || |     |||| | | |  | |   |  |  |    | |      ||||     |   | |||||  |||||||||| ||||||||||||||| | || |||| ||| || || ||||| ||||||||  |  | || || |||||  | || || || ||||| |||| 
cattttatccaatgtaaatggtctgtgggcttttgttactgca-atataatccgccgaatgggaattttaatctttgaatgtacg-tggatgtgtttggcagATCCAACGTATATGATTCGAGCTGTGCCTAGCATTGCATCGGATAACGTCTACTGCACTTTGTTGGCACATAGTGCCATCCACGGTGCTATGGCTGGTTT

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|298172807|gb|HO019791.1|HO019791
EST:     GATCATTTTGCTGCACAGAAGACCCTGCCCATAACTCTCAAATACATAG                         ATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
genomic: GATCATTTTGCTGCACAGAAGACCCTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
EST: gi|16349349|gb|BI974944.1|BI974944
EST:     GATCATTTTGCTGCACAGAAGACCCTGCCCATAACTCTCAAATACATAG                         ATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
genomic: GATCATTTTGCTGCACAGAAGACCCTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
EST: gi|207796392|gb|GD769742.1|GD769742
EST:     AGAAGACCCTGCCCTATTAACTCTCAAATACATAG                         ATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
genomic: AGAAGACCCTGCCC-A-TAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
EST: gi|33390216|gb|CA853423.1|CA853423
EST:     GATCATTTTGCTGCACAGAAGACCCTGCCCATAACTCTCAAATACATAG                         ATCCAACTTATATGATTCGAGCTATTCCAAGCAA
genomic: GATCATTTTGCTGCACAGAAGACCCTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAA
EST: gi|208212784|gb|GE013257.1|GE013257
EST:     ACCCTGCCCATAACTCTCAAATACATAG                         ATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
genomic: ACCCTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
EST: gi|207706215|gb|GD688845.1|GD688845
EST:     ACCCTGCCCATAACTCTCAAATACATAG                         ATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
genomic: ACCCTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
EST: gi|207706215|gb|GD688845.1|GD688845
EST:     ACCCTGCCCATAACTCTCAAATACATAG                         ATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT
genomic: ACCCTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                  ccttctctttatgttt  CT-rich tract
                                         tttatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA