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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG

Basic information

species Glycine max
transcript GLYMA09G41330.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
ttttatctgagat-caataattaatttgcatgctagacatgtctttatgctgattgg---tcatttat-ctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
 ||    |||  | || ||  | | | ||   |||   ||   || || || ||| |   | ||||||  |  |||       |   || ||| |   |   |||||||||||||| ||||| ||||| || || |||||||||||||| || || || |||||||| || || |||
cttagattgatttacactatgtcagtggcgcacta--tataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttca---taaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG

upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 2
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgc-tgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
|     ||||| | | ||     | |   | ||  |   ||    |    | |    |    ||| ||   |  ||   |   || | |         |||||||||||||| ||||| ||||| || || ||||| |||||||| || || || |||||||| || || |||
tgcacactgaggtta-tagcatctctatctactccatccgttccaaaatataagcactgtaatatatgttttagtttgctaactcctcttttcacaaacagCGTTTTGCTGCAGTTATCATGAGAATAAGAGAACCGAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG

upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
----------------------------------ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctg-attggtcat-ttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG----------------------------
                                  || | || |  |  ||  |   | || ||||  |    | |  |    ||| ||   |  | | || |  |     ||  | |||| ||||        |||||||||||||| ||||| |||||||| ||||| ||||| || || || || || ||||| || || ||||||                            
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC

upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
ttttatctgagatcaataattaatttgcatgctagacatgtcttta---tgctgattggtcatttatctgcagtgcttatgtctatcttttga-atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
         | |||   |  |  ||   ||   ||  || | |||    | |  ||| ||      | |    |   ||| |  |  || |||  |   |||||||||||||||| || || |||||||| ||||| |||||||| || ||  | || ||||| ||||| ||||||
----gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG

upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttg----cagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
  ||   |    || |   ||| | |  || |||  ||| | || ||  |  | |     ||| ||    |||| |   |  | ||  | |   |||    ||||||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||
--ttgaatatcgtcga-gtttactattgatactattcatttgttgatatttttggtgttgttacctatt-tgctcaacgccttgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG

upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 2
--ttttatc-tgagatcaataattaatttgcatgctagac--atgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
    || || |||   |||    || | ||  |   || |  ||    ||    |   |  | ||| | |    | | |  ||  |||  |     | ||  ||||||||||| |||||||| ||| | |||||||| || ||||| ||||| || ||||||||||| || || |||
ctggttgtcatgaagacaacttgtactgtgtttctcaggctgatactgttgcttttgcttcttattcacccaatgcgttggtgggtattgt-----tgttcacagCGTTTTGCAGCTGTTATCATGCGAATCAGGGAGCCTAAAACAACTGCTCTTATTTTTGCATCCGGTAAAATG

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|254336235|gb|GR842414.1|GR842414
EST:     AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAG                         CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC
genomic: AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAGgcaagttttg ... atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC
EST: gi|254334604|gb|GR844389.1|GR844389
EST:     AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAG                         CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC
genomic: AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAGgcaagttttg ... atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC
EST: gi|19270744|gb|BM887000.1|BM887000
EST:     AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAG                         CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC
genomic: AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAGgcaagttttg ... atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC
EST: gi|21887668|gb|BQ740881.1|BQ740881
EST:     AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAG                         CGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC
genomic: AGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAGgcaagttttg ... atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
 tgctgat  putative branch site (score: 3)
                                              tctttgc  putative PPT
           tcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - - -acatgtc
- - - - - - - - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg