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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctagaataataccattttaaccatattttaactgtgcacactcaaaagagaaattgaagaatttccatcatcatgtatataactaatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA

Basic information

species Glycine max
transcript GLYMA05G32510.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g35010.1 (Oryza sativa), 3'ss of exon 4
gtatgctagaataataccattttaaccatattttaactgtgcacactcaaaagagaaattgaagaatttccatcatcatgtatataactaatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA
          | |  | || ||| || | |||||   ||||     |||    |     ||||   | ||  | | | |     |  ||||| || |    | |   ||||  || ||| | || ||  | ||| |||||||||| ||||| ||||| || ||||||||||||   ||||| ||| |||||||||| ||||| ||||  |
------ggagacaccatcagttttacta-attttg--tgtgattgttcactt-attttctgaaagttctcattaagctttggcttgcctaatttaaacaattttgagcagGCTGATGAAGCTCTGTCCATCTATCTGGAATATGTTTCTGGAGGTTCAATTCATAAATTACTTAGAGAGTACGGTCCATTTAAGGAACCTGTGATTCGTA

upper sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------gtatgctagaataataccattttaaccatattttaactgtgcacactcaaaa------gagaaattgaagaatttccatcatcatgta--tataac-taatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA
                                                                      |  |  ||||  || | ||||  | | ||   | || |   || ||           ||  | || |   | |   | | | |||   | |||| |  |  ||   |||||| |||||  |||||| |||| || || |||||||| |||||||||||||| |||||||| || |||||||| || |||||| | |||||||| ||||| |||||||
gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgcaatctctttccaatctgttcattccaagtgagtggacggtgtatttgaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA

upper sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36728 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctagaataataccattttaaccatattttaactgtgcacactcaaaagagaaattgaagaatttccatcatcatgtatataactaatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA
                                                           |    ||  ||||      || ||  ||  | |  |  | |   ||||||| | || ||     | | | | ||  | || ||||| || || || || || || ||  | ||||||||||||||| |||| ||||||||||| ||||  |
----------------------------------------------------------gtagtcaagctccactt---tgcattcaagca-tgaacgttcg-attttcagATGGAGGATGGCTTATATATTTACCTCGAGTATGTGTCCGGGGGATCGATTCACAAGCTTCTTCAGGAGTATGGTGCATTCAAGGAGCCTGTGATTCGCA

upper sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ27940 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctagaataataccattttaaccatattttaactgtgcacactcaaaagagaaattgaagaatttccatcatcatgtatataactaatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA
                                                           |    ||  ||||      || ||  ||  | || |  | |   ||||||| | || ||     | | | | ||  | || ||||| || || || || || || ||  | ||||||||||||||| |||| ||||||||||| ||||  |
----------------------------------------------------------gtagtcaagctccactt---tgcattcaagcatta-acgttcg-attttcagATGGAGGATGGCTTATATATTTACCTCGAGTATGTGTCCGGGGGATCGATTCACAAGCTTCTTCAGGAGTATGGTGCATTCAAGGAGCCTGTGATTCGCA

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|15287318|gb|BI471209.1|BI471209
EST:     TAAATCAGCTTTCACACCCAAATATTGTTCAATACTATGGGAGTGAACTG                         GTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
genomic: TAAATCAGCTTTCACACCCTAATATTGTTCAATACCATGGGAGTGAACTGgtatgctaga ... atgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
EST: gi|254325845|gb|GR838726.1|GR838726
EST:     TAAATCAGCTTTCACACCCTAATATTGTTCAATACCATGGGAGTGAACTG                         GTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
genomic: TAAATCAGCTTTCACACCCTAATATTGTTCAATACCATGGGAGTGAACTGgtatgctaga ... atgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
EST: gi|22521983|gb|BU080794.1|BU080794
EST:     TAAATCAGCTTTCACACCCTAATATTGTTCAATACCATGGGAGTGAACTG                         GTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
genomic: TAAATCAGCTTTCACACCCTAATATTGTTCAATACCATGGGAGTGAACTGgtatgctaga ... atgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
EST: gi|6567062|gb|AW234689.1|AW234689
EST:     TCACACCCTAATATTGTTCAATACCATGGGAGTGAACTG                         GTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
genomic: TCACACCCTAATATTGTTCAATACCATGGGAGTGAACTGgtatgctaga ... atgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgaagaatttccatcatcatgtatataactaatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA
                              aactaat  putative branch site (score: 2)
                                              tgttttc  putative PPT
                atcatcatgtatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctagaataataccattttaaccatattttaactgtgcacactcaaaagagaaattgaagaatttccatcatcatgtatataactaatatatatccatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTTCATTTAAGGAGCCTGTTATTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG