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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

Basic information

species Glycine max
transcript GLYMA01G00870.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
---------------------------------gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaag----agtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                 |    |   || |   ||||    | | ||  | | || |   |    |             ||| |    | |||   | | |  |||||  |   ||||||||||||| |||||||| || |||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| |||||||| || ||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttt-tatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatg-gcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtttgtaa--agattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaa-gagtaatgcc-ttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
    ||||  |  ||       ||  | || | ||   ||||||   |   |   |       || |   |||  ||   ||| || || |  ||| ||||||| ||||| |||||||||||||||||||||||||| || ||||| || |||||||| || || || || |||||  ||||||| |||||||| || ||
----gtaactatgtttgcttcacacaggataaggttgttacacatcttattactggtctctattgtactaagttgtgaagttccctattattatttgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaag-agtaatgcct----tctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
           | |   |    |   ||| |   | ||  ||  |  |     ||      | |  | |  ||   ||    |||  |   | | || ||||||| || || ||||| || || ||||| |||||||| |||||||| ||||| ||||||||  | || || ||||  ||||||||||| ||||| || ||
----------gtcagtcgcctcttttattctactttta-gcatcccaagctttgcttgatttcactgtaacaaaatctcagatcttatgcttctattgcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
--gtttgtaaagattaaaagttcatgga-attatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
    | ||     ||   | ||  || |     |||  ||    |   |  |    |  | ||        | | ||||| |  |||| |  | |  ||||||||| || |||||||| ||||||||||||||||| || ||||| || || ||||| || || || || |||||  ||||||| |||||||| || ||
gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctgccatttttt--tatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
          | | |   |   ||| || |||  ||       || | ||| |    | ||   ||   |      | || || ||  |  | |||||||||| || ||||| || || ||||| ||||| |||||||| || || ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
-------gtcagtgattttctctggtatcatgcttgctt---tacggcaagaattgctagcatcaaatatctcagatgctgttatcc-tactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
    |||   |||   |  || |    ||   | |  | | |     ||   |    | | |      || |     | ||  |     ||  ||||||| || || ||| |||| ||||||||||||||||| || ||||| || ||||| |||||||| || || |||||  | ||||| |||||||| || ||
----gtagccatttgtaactcttatttttgc-tattgatatagttgtaacacatttctagattggtctgtgacaatat-tccatcggaattggcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                 ||   |||  || |  |    || |          || | ||   |  | |   ||  |   | |||  | |  | |||||||||| || ||||| || || || ||||||||||| ||||| ||||| || |||||||| || ||||| || |  || |||||||| ||||| || ||
-----------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtttgtaaagattaaaagttcatgga-attatgtgtgtacacacactgaaag-gagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                 |||  |  | | ||| | | || | | |  |||   | ||||||||||    |   | |   |    ||| ||| |  ||||||| || ||||||||||| ||| ||||||||||||| |||||||| || || ||||||||||||||||||||||| |||||||||||||||||||| ||
-----------------gtttgtatacactatctttcta-atatatagaagctgggcaatggctggtctaaccaagtgctgcactttttgtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaat--ggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                  ||  |      |      || ||    ||| |   |  |    ||   ||  |   |  ||||  || |  | | |  || |       || | |||||||||| || ||||| |||||| ||||||||||||| ||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtac--tcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------------gtttgtaaagattaaaagtt-catggaattatgtgtgtaca---cacactgaaaggagcaatggctgaaagagtaatgccttctcttttct-gttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                                             | |||  |  ||  |   |    ||||||   |   | |    |||    |  |      ||  |   | |  | |||    | |    | ||| | ||||||| || |||||||| ||||| |||||||||||||| || ||||| || ||||||||| | || ||||| || ||  | ||||| || |||||||| ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgataagactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                              |  |||   ||    |           |  ||       |  |  ||      || || ||| |||||||||| |||||||||||||| || |  ||||| ||||| ||||| || |||||||| || || ||||| |||||  | || ||||||||||| || ||
-----------------------------gtcagtgcctacgtgtt-----------tttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ23976 (Selaginella moellendorffii), 3'ss of exon 11
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                                          || ||          |  ||       |  |  ||      || || ||| |||||||||| |||||||||||||| || |  ||||| ||||| ||||| || |||||||| || || ||||| |||||  | || ||||||||||| || ||
----------------------------------------gtcagtgcctacgagtttttcttgccttctcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

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|192321851|gb|FK013229.1|FK013229
EST:     GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAG                         ATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
genomic: GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
EST: gi|192321852|gb|FK013230.1|FK013230
EST:     GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAG                         ATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
genomic: GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
EST: gi|6725492|gb|AW309891.1|AW309891
EST:     GATCATTTTGCTGCACAGAAGACACTGCCCA-AGACTCTCAAATACATAG                         ATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
genomic: GATCATTTTGCTGCACAGAAGACACTGCCCATA-ACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
EST: gi|7693069|gb|AW761167.1|AW761167
EST:     GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAG                         ATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
genomic: GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGT
EST: gi|6566092|gb|AW233852.1|AW233852
EST:     GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAG                         ATCCAACCTATATGATCCGAGCT
genomic: GATCATTTTGCTGCACAGAAGACACTGCCCATAACTCTCAAATACATAGgtttgtaaag ... tgttttacagATCCAACCTATATGATCCGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA
                               tgccttctcttttctg  CT-rich tract
                                             tgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

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