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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtccctaactccacagatctattggaaattttatgttcttcttttgaaatcaacttcatgcattttattctatggaattcttgaagaaatgacatgattagatataagatgtgttcagttttatcctttatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGAAAAGGAAGCTGAAGAAGAGA

Basic information

species Glycine max
transcript GLYMA14G12380.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G12380.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G140160_T03 (Zea mays), 3'ss of exon 5
gtattgtccctaactccacagatctattggaaattttatgttcttcttttgaaatcaacttcatgcattttattctatggaattcttgaagaaatgacatgattag-atataagatgtgttcagttttatcctttatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGAAAAGGAAGCTGAAGAAGAGA
                                      |   |||||| ||||  |   | ||   |  |     |   | |     | || | ||     ||  | ||||   |    |   | ||| |  | | |     |||| ||| |||| || || || ||||| ||||||||||||   || ||||| ||||  ||||||||| ||||||||||||||| |||||  |||||||| |
-------------------------------------gtaaacttcttgtgaaccc---tgcagataaataggcttgaagtagaggagcagcattgttgcaatcggtatatctaaccaatcgtgattttttttgtttcatttagGACGAGAACAACTCCTGCCCTATCTGCCGGCATGAGCTGAGGACGGATGACCATGTGTATGAGAGCAGGAAGGAGCGTGAAAGGGAAGAGGAAGAAGATA

upper sequence: GLYMA14G12380.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g02290.t01 (Vitis vinifera), 3'ss of exon 4
gtattgtccctaactccacagatctattggaaattttatgttcttcttttgaaatcaacttcatgcattttattctatggaattcttgaagaaatgacatgattagatataagatgtgttcagttttatcctttatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGAAAAGGAAGCTGAAGAAGAGA
||| ||| ||| |  |     ||  ||   ||  ||   |       |  ||  ||  ||| |||| ||  | |   ||  |||  |  | || |    |   | | |    ||  | |||  |||            |||||||| ||||||||||||| || |||||||||||||| ||||  |||||||||| ||||||||||||||||||| || | || ||||| || ||||||||||
gtaatgtacctcatcctt---attcatcataatattagagaagaaactcagagctcctctt-atgc-ttccact---tgccatttgtctaaaatttggctttctcgttcctggacat-ttcgcttt------------ggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGATCGTGCCTATGAGAGCTGGAAGCAGAGGGAGAAGGAGGCGGAAGAAGAGA
















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|20498860|gb|BQ273790.1|BQ273790
EST:     AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
genomic: AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
EST: gi|31465459|gb|CD407487.1|CD407487
EST:     AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
genomic: AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
EST: gi|192320474|gb|FK012332.1|FK012332
EST:     AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
genomic: AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
EST: gi|193510240|gb|FK467578.1|FK467578
EST:     ACCCACCATGTCTAAAGCCTATTGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGA
genomic: ACCCACCATGTCTAAAGCC-A-TGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGA
EST: gi|22927277|gb|BU544416.1|BU544416
EST:     AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
genomic: AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
EST: gi|58018057|gb|CX704799.1|CX704799
EST:     AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
genomic: AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
EST: gi|31466528|gb|CD408556.1|CD408556
EST:     AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACCATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
genomic: AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
EST: gi|208258702|gb|GE057081.1|GE057081
EST:     TTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCCGCAAACTGATGAT
genomic: TTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
EST: gi|6913301|gb|AW394831.1|AW394831
EST:     AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTG                         GATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT
genomic: AGTTGCCATGCAAGCACACATTCCACCCACCATGTCTAAAGCCATGGCTGgtattgtccc ... tatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaatgacatgattagatataagatgtgttcagttttatcctttatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGAAAAGGAAGCTGAAGAAGAGA
                                   ttttatccttt  CT-rich tract
          atgattagatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtccctaactccacagatctattggaaattttatgttcttcttttgaaatcaacttcatgcattttattctatggaattcttgaagaaatgacatgattagatataagatgtgttcagttttatcctttatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGAAAAGGAAGCTGAAGAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA