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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttgcttcctcaattcactttgttttttgaaccatgattttttatcatgtcatattaatgttttttgtttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC

Basic information

species Glycine max
transcript GLYMA16G08470.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 1
-------gtttttgcttcctcaattcact--ttgttttttgaacc---atgattttttatcatgt-----catattaatgttttttgtttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC
       |  ||   |  | |  | | ||  | ||| | || |     ||  ||||| | ||| |     | ||   |  | |||  |  || ||  ||||||||| ||||||| || || ||||| || ||  ||||||||||||||||||| || ||||| || |||||||| |||||||||||||||||    ||||
actttcagacttcattgtcactgtgctctgctggttctatgtattttaatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC

upper sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 1
---------gtttttgcttcctcaattcact-ttgttt---tttgaaccatgattttttatcatg-tcatattaatgtt--ttttgtttttgtttt-tagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC
          | ||||    ||||| ||  | |||  |   || | |  |    | | ||||||  || | ||  ||       ||||||| |||  ||||||||  ||||||| || || ||||| |||||  ||||||| |||||||| || |||||||| || |||||||| ||||||||||| |||||    ||||
gaagtttccatgtttgacagctcaaatctttgttggctctgttcgtaaaaaagctctgtatcatactcttcttcctgaaaacaatgtttttatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAAGAGTTCATGGATGAAGTTTTTGCCCAGAGCAAGAAGTTCTTTGACCTTC

upper sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------gtttttgcttcctcaattcactttg--ttttttgaaccatgat----------tttttatcatgtcatattaatgttttttgt--ttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC
                                        |||||   ||    |||  | ||||  | || |||| | ||||          ||||| |  ||    | | ||| | |  ||  || ||  || |||||||||||||||  || |||||||| ||  |||||||||| |||||| | || |||||||| || ||||| |  |||||||||||  | ||  ||||||
gtttgtctcccatctcagtttttcgattttgcatgttgttgttttcttttgacaaatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC

upper sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 1
---gtttttgcttcctcaattcac--tttgttttttgaaccatgattttttatcatgtca---------------------tattaatgtt---ttttgtttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC
     |||||  |||    | | |  |||| ||   ||   | ||      |  | |  |                     | ||||| ||   || || |||    || |||||||||||||||| || || ||||| ||  ||||||| ||||| ||||||||||| ||||| |||||||| || || ||||| |  || ||| || | |
gtgcgttttgtatccaagctcctccgtttggttgccgagaaaggagaaagaaggaagggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC

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|298183235|gb|HO028220.1|HO028220
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
EST: gi|24135790|gb|BU926300.1|BU926300
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
EST: gi|298181471|gb|HO022910.1|HO022910
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
EST: gi|298166108|gb|HO009079.1|HO009079
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
EST: gi|298179589|gb|HO026970.1|HO026970
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
EST: gi|19345789|gb|BM890669.1|BM890669
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
EST: gi|151412168|gb|EV281980.1|EV281980
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
EST: gi|254340856|gb|GR854584.1|GR854584
EST:     TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAG                         GCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG
genomic: TCGACCTCTCCAACCCTGACATCAACCAATCCGTCAATTTACTCAAACAGgtttttgctt ... ttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaaccatgattttttatcatgtcatattaatgttttttgtttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC
                           tattaat  putative branch site (score: 2)
                                   ttttttgtttttgttt  CT-rich tract
           attttttatcatgtca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttgcttcctcaattcactttgttttttgaaccatgattttttatcatgtcatattaatgttttttgtttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA