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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggaaccaggtagcagatttactagcccccctcctgttcctggttcttgatgaagcatttttttttgttcttgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA

Basic information

species Glycine max
transcript GLYMA09G37080.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 8
aatggaaccaggtagcagatttacta-gcccccctcctgttcctggttcttgatgaagcatttttttttgttcttgatcatgagtaaac-atttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
 ||  |      |  ||| ||| | | |  |   || ||        |     |  ||  | ||    |  ||||     |||  ||||  |||| ||||||| |||| ||||||| ||| ||||| | ||||| | || ||||| |||||||||||||| || || |||||||||||||| ||||||||||||||||||||
-atctattttactt-cagcttttcaatgatctaatcatgcattgcaataccattttagtttattggagttatcttataattgaaaaaactgttttattgcagACATCACAACGGCAGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g25980.1 (Oryza sativa), 3'ss of exon 8
aatggaaccaggtagcagatttactagcccccctcctg--ttcctggttcttga--tgaagcatttttttttgttcttgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
  |   | |       | || | || |  |   |  ||  ||| ||    || |  | |  ||||||||  || |||   |  | | ||  ||||    | ||||| | |  || || |||| ||| |  |||||  | || ||||||||||| || ||||||||||| |||||||| || || ||||| ||||||||||||||
ctttacatcgtaacaaacatgtgcttgttctgtttatgatttcatgtgctttaaattcagacattttttcatgatctgact--tcatta--cattaccattcagATGTAACTACAGCTTCAGTTGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGTGGCTACTGTAAGCTCCACCTGTCATATTCTCGTCATACTGA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
aatggaaccaggtagcagatttactagcccccctcctgttcctggttcttgatgaagcattttttt----ttgttcttgatcat--gagta--aacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
     |      | ||  |||     |   ||| | ||  | |||| ||  |  |   || ||  |       | | |  ||||  || ||  || || |||||  |||||| | ||| ||| | | ||||| | ||||| | ||||| || ||||||||||||||||| || |||||||||||||| ||||||||||||||||||||
-----agtggtattgctaattct---gtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G082174_T03 (Zea mays), 3'ss of exon 9
aatggaaccaggta-gcagatttactagcccccct--cctgttcctggttcttgatgaagcatttttttttgttcttgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
       | || |  |         |||||         | |   |  |  |||||| | ||  |   |  |||| |  | |  |  ||| || |||||  |||||| |  || ||| | | ||||| | ||||| | ||||| || ||||||||||||||||| || |||||||||||||| ||||||||||||||||||||
ggaattgctagttctgtttcccccttagccatggaaatatatcattaatatttgatgta-caaatacataggttcatc-tgactaacaaa-atctttttttagATATAACTACCGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
--aatggaaccaggtagcagatttactagcccccctcctgttcctggttcttgatgaagcatttttttttgttcttgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
    |   || |   |      | | ||   |   | |   |  || || |  ||  |   | ||  | ||    |||| | |  |   | ||    |  |||| | |  || ||  | |  || |  |||||  | || ||||||||||| || ||||| ||||| ||||||||||| || |||||||| |||||||||||
actttctcactaaacatgcagctgattatttcattttcccatg-tgcttttctatagaaattattcatctgaatctgattaagtcttt-ctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 8
aatggaaccaggtagcagatttactagcccccctcctg-ttcctggttcttgatgaagcatttttttttgttcttgatca--tgagtaaaca-----tttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
            |   |  | ||| | |        || ||     || |   |  | |   |   |    |  ||  ||    | | | |      ||| ||| ||||| ||| ||| ||| ||| ||| | ||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
--------tcaattttatttctaccaccatagggaatggttggcaattttatttatatctcatccctccactgctgggcagacaaatgatctgttgttttctttccagATGTCACAACTGCAGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
aatggaaccaggtagcagatt-tactagcccccctcctgttcctggttcttgatgaagcatttttttttgttct-tgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
| ||  |  || |   ||||| | || |      |  |    | |  | || ||   |   |   |    | |   ||   |  |      || || | |||||||    || |||   |  || | |||||| || || || || ||||| || ||||| || |  || ||||||||||||||||||||||| ||||||||
agtgtcaagagctctgagattgtgctggatggtttatta--gcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA

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|207809609|gb|GD782313.1|GD782313
EST:     TGCTATATTTGAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTG                         ATATCATAACGGCATCAGCTGCTAGA
genomic: TGCTATATTTGAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGA
EST: gi|207784087|gb|GD758397.1|GD758397
EST:     AAACTCAGGCACTAATTCAGTACCCTG                         ATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
genomic: AAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
EST: gi|58024389|gb|CX711130.1|CX711130
EST:     GCTATA-TTGAAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCNTG                         ATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
genomic: GCTATATTTG-AAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
EST: gi|208178396|gb|GD977005.1|GD977005
EST:     AAACTCAGGCACTAATTCAGTACCCTG                         ATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
genomic: AAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
EST: gi|58014314|gb|CX701056.1|CX701056
EST:     TGCTATATTTGAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTG                         ATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
genomic: TGCTATATTTGAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
EST: gi|193377459|gb|FK340157.1|FK340157
EST:     AAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTG                         ATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
genomic: AAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
EST: gi|58017755|gb|CX704497.1|CX704497
EST:     TGCTATATTTGAAAAGAATGGTCAAGCTCAGGCACTAATTCAGTACCGTG                         ATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
genomic: TGCTATATTTGAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT
EST: gi|7283672|gb|AW596276.1|AW596276
EST:     TGCTATATTTGAAAAGAATGGTCAAACTCAGGCGCTAATTCAGTACCCTG                         ATATCATAACGGCATCAGCTGCTACAGAAGCTCTAGAGGGGCATTGCATAT
genomic: TGCTATATTTGAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTGgtattaatca ... ttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgatgaagcatttttttttgttcttgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
                         tcttgat  putative branch site (score: 4)
                                          cattttttt  putative PPT
             atttttttttgttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggaaccaggtagcagatttactagcccccctcctgttcctggttcttgatgaagcatttttttttgttcttgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - ccccctc
- - - - - - - - - - - - - - - - - -ctgttcc
- - - - - - - - - - - - - - - - - - - - - - - -cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgag