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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacactggtgccttgtgttttttttttttgagaaattatatttttaactggattttcattttatggctattcttatgttggttattcttatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG

Basic information

species Glycine max
transcript GLYMA05G04160.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G337631_T01 (Zea mays), 3'ss of exon 5
gtagacactggtgccttgtgttttttttttttgagaaattata-tttttaactggattttcattttatggctattcttatgttggttattcttatttata-agGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG
   ||      | ||       | |  | |   |  | | | |     | | | ||| |||| |  |     ||||   | |||| |  | |||    |  |||  || |||||| |||||| |  | | |||||  | |||||||| ||| | |||||||| ||||||||||||||||| || ||||| ||||||
-atgatgtgcttaccaaacaggtatagtgtaccatgattgagagcacatgaattgatattcagtaaacaa--attcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTCCCTGCTGGGATGCTAGATGATGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG

upper sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G069008_T02 (Zea mays), 3'ss of exon 3
gtagacactggtgccttgtgttttttttttttgagaaattatatttttaactggattttcattttatggctattcttatgttggttattcttatttata-agGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG
            |  | ||||    |  ||  ||| |  |  |||        ||| |||| |  | |   ||||   | |||| |  | |||    |  |||  || |||||| |||||| |  | | |||||  |||||||||| ||| | ||||| || ||||||||||||||||| || ||||| ||||||
------------gtatagtgtaccatgattgagagcacatgaatt--------gatattcagt--aagaaaattcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG

upper sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagacactggtgccttgtgttttttttttttgagaaattatatttttaactggattttcattttatggctattcttatgttggttattcttatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG
                 || | | | ||| |       |  | || ||  ||  |||||      | |   |   ||||   |||| ||     ||  ||||   ||||||||  ||| |  |   || ||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| || |||
-----------------gtatctctatttat-----gttcgtgttgtt--ct--attttttaacaaagatcaacattatacgggttgtt-----ttggaagGTTCGGGTTCCTACTGGGAAGATTGTTCTGGAATTACCTGCTGGAATGTTGGATGATGATAAAGGTGACTTTGTTGGTACTGCAGTTCGCGAG

upper sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g04840.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------gtagaca-ctggtgccttgtgttttttttttttgagaaattata-----------tttttaactggattttcattttatggctattcttatgttggttattctt--atttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG
                                                    |  |||  |  |   ||||  | ||     || | |||  | |           |   ||  |  ||  |  | || |         | ||      | || |  || | |||||  ||||| |||||||| |     || ||||||||||| ||||||||||||||  |||||| |||||||||| |||| || ||||  ||||||
gtaggtttttcatgttcatcagtgttctttatgatgcactacttcaatttcctgaacaattaatcaattgttatcttagaaattaaaaaaaaaaaggagagagaaataactatttaaatgcttttattttcttccaaactctgacaaacactcatgcatgtgtaagGTTAGGGTCCCTGTTGGGAAGCGTATCTTGGAATTGCCAGCTGGAATGTTGGAAAATGACAGAGGTGATTTTATTGGCACAGCAGCTCGTGAG

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|21677977|gb|BQ630328.1|BQ630328
EST:     TGATACTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG                         GCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTG
genomic: TGATACTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAGgtagacactg ... tatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTG
EST: gi|15813432|gb|BI785707.1|BI785707
EST:     TGATACTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG                         GCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTG
genomic: TGATACTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAGgtagacactg ... tatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTG
EST: gi|22933275|gb|BU550414.1|BU550414
EST:     TCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG                         GCAAGGGTTCCTGTTGGAAGAAACATTNNNGAATTGCCTGCTGGAATGTTG
genomic: TCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAGgtagacactg ... tatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTG
EST: gi|298173390|gb|HO016726.1|HO016726
EST:     TGATACTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG                         GCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTG
genomic: TGATACTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAGgtagacactg ... tatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaactggattttcattttatggctattcttatgttggttattcttatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG
 ttttaac  putative branch site (score: 2)
                                         ttcttattt  putative PPT
                                      ttattcttatttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacactggtgccttgtgttttttttttttgagaaattatatttttaactggattttcattttatggctattcttatgttggttattcttatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG