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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG

Basic information

species Glycine max
transcript GLYMA07G00490.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaatta-tcaatttgttgtttattagctg-agtgttcttctttttgtcacct------cagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
      |||     |  | || | |   ||||||  ||    |||  ||||   ||   |   | | ||   | |  ||  || |||| |||||   ||      ||| ||||||||||||||||||  ||||||||  |||||||||| ||||  |||||||| || || || ||||||||||||||||| ||||||||||||||||
------tttatttcttgtctgctacgtcttctataatta--tagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG

upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 1
ggaaaattt-----tgaagtgctatgtt-tcaaattctattgtttatcagccgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
  ||   ||       || || | |||  ||  | |  | ||  | | |   | | | |  | |||||      |   || |  |||| |  |||        ||| |||||||||| ||||||||||| |||||  ||||||| ||||| |  || ||||| || || ||| ||||||||  |||||| ||||| ||||||||||
ataatgcttgtcagctaactgttttgtgatcgtagttgaatgagttttattggcattcaatattttgtcaaggttctactaaaggttccttattta------ccagATTATGGCTGTGAAGAAGAATATAGAAGAGATACAAGGGAAAGACAGCTATCCATGGGGCCAACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATG

upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaattatcaatttgt---tgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
  |   ||||    | | |||      ||    |   | |           ||| | ||  |   || ||||   ||| |  || ||||  ||  |     || | ||||| || ||||||||||||||||||  |||| | ||||| || || || ||||| |||||||| |||||||||||||| ||||||||||||||||
--agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctg-gaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG

upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
ggaaaattttgaagtgctatgtttcaaattctatt--gtttatc--agccgaaattatcaatttgttgtttattagctgagtgt-tcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
    | |  | || |  |   |  | ||| | ||   ||||     ||  ||   | | | | |     | ||||  |  | |  |  | |  ||||    | || | ||||| || ||||||||||| ||||||  |||||||||||| ||||| |||||||| ||||||||| ||||||||||||| || |||||||||||||
----actgctaaaattatgactcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtt-tttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG

upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 1
ggaaaattttgaagtgctatgtttc----aaattctattgttta--tcagccgaaattatca-atttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
     | | ||     || |||| |    ||||    |||  |   |  |  | ||  | || ||   ||  | |  | ||  ||  |    | |||   |    |||||||||| || ||||| || ||||||||||||||||||||||| || || || ||||| || |||||  ||||||| ||||| ||||| ||||||||||
-----actctgttcatctgtgttcccatgaaatatatttgcctgagtgtgttgcaaacaccacatgacttaatgaaaaccttggtaattgcttgttta--attgaagGTTATGGCGGTAAAGAAAAACATTGAAGATGTACAAGGAAAAGACAACTATCCGTGTGGGCAACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATG

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|8827362|gb|BE211092.1|BE211092
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298188098|gb|HO032055.1|HO032055
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTCCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|213614987|gb|DB957039.1|DB957039
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298164323|gb|HO013968.1|HO013968
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAACATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|213592873|gb|DB969839.1|DB969839
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298167381|gb|HO012644.1|HO012644
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|27427422|gb|CA938942.1|CA938942
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|23727295|gb|BU761676.1|BU761676
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|13125598|gb|BG316168.1|BG316168
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298172529|gb|HO019569.1|HO019569
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|33387852|gb|CA851059.1|CA851059
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|15200810|gb|BI424534.1|BI424534
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|15338030|gb|BI498686.1|BI498686
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298164600|gb|HO014245.1|HO014245
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
                                tgttcttctttttgtc  CT-rich tract
     ttatcaatttgttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG