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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttaccatctctttctcccccactatttggaacatttccttatcttgattaactagactctccatgttgttccttatctaattttttcatcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATTACTTCTGCTGCTGTAAAGAAAGCTTACAGGAAGGCCACCCTTTGTGTCC

Basic information

species Glycine max
transcript GLYMA16G25190.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25190.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g50370.1 (Oryza sativa), 3'ss of exon 6
--tttttaccatctctttctcccccactatt-tggaacatttcc---ttatcttgattaac-tagactctccatgttgttccttatctaattttttcatcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATTACTTCTGCTGCTGTAAAGAAAGCTTACAGGAAGGCCACCCTTTGTGTCC
     | || || | |   ||||       | |  |||  |||      |   |||  ||| || |  ||   | |  |   || | |     ||||  | || |||||||||||  |||| ||||| ||||||||| | ||||| |||||  | |||||  |||||||||| |||||||| ||||||||||| |||||||||||||
gtaagtgactatttgtaaatcccaggaagctgtaaaaccattctgagagactatgacaaacatataacctttttttaatcttttttttctccatttctccctggcagATTCTTGGAGCTGACAGTGGTTGGCAGCCAGTGCCACTTACAGAGCTAATTACAGCTGCTGCTGTGAAGAAAGCCTACAGGAAGGCAACCCTTTGTGTCC

upper sequence: GLYMA16G25190.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G438895_T01 (Zea mays), 3'ss of exon 8
tttttaccatctctttctcccccactatttggaacatttccttatcttgattaactagactctccat---gttgttccttatctaattttttcatcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATTACTTCTGCTGCTGTAAAGAAAGCTTACAGGAAGGCCACCCTTTGTGTCC
                 |   |  |||  |   |    ||||||      | |  ||||   |  |    ||| |  | | ||    | ||||  | || |||||||||||  | |||||||||||||| ||  | ||||| |||||  |||||||  | | |||||| |||||||||||||||||||| ||||| |||||||
----------------gtaagcagctaaatttcatgcatccttaaacccgtaacatagaacatggaaaaggttatcacgtgtcgctctgtttc-ccctggcagATTCTTGGTGCCGATAGTGGCTGGCAACCGGTGCCACTAACAGATCTCATTACAGCGGTTGCTGTGAAGAAAGCTTACAGGAAGGCAACCCTATGTGTCC

upper sequence: GLYMA16G25190.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G316635_T03 (Zea mays), 3'ss of exon 5
tttttaccatctctttctcccccactatttggaacatttc-cttatcttgatt---aactagactctccatgttgttccttatctaattttttcatcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATTACTTCTGCTGCTGTAAAGAAAGCTTACAGGAAGGCCACCCTTTGTGTCC
 |  |||     |  ||| ||  ||| |   |  | |||| || |  |||| |   ||  |||| | |  |    |     || |  ||| ||| ||| | ||||| |||||  | || |||||||||||| || | || ||||||||| | || ||  |||||| ||| ||||| || ||||||||||| |||||||||||||
gtactacttaaaccatctacca-actctagaggccctttctctgaatttgacttcgaatcagacac-cagtccaatcatgcattt--tttcttcttctgggcagATACTTGGTTCAGACAGTGGCTGGCAGGCAGTTCCCCTCACAGACCTTATCACAGCTGCTGGTGTCAAGAAGGCATACAGGAAGGCAACCCTTTGTGTCC

upper sequence: GLYMA16G25190.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g02070.t01 (Vitis vinifera), 3'ss of exon 6
tttttaccatctctttctcccccactatttggaacatttcctt---atcttgattaa---ctagactctccatgttgttccttatctaattttttcatcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATTACTTCTGCTGCTGTAAAGAAAGCTTACAGGAAGGCCACCCTTTGTGTCC
      | | |      |     | ||| ||   | | |   |   || ||  ||||   | | | |     ||   ||  | | ||   ||||   | ||| ||||| || || ||||||||||| ||||| ||||| ||| | || || || || ||| ||| |||||||||||||||||| || || ||||| |||||||| |
------caaacaacaaatgaatgaatatctgattcttctgtcttcaattttcgttaaactccaaaatgctattgacatttttaaacttgattttctttattggcagATCCTAGGACCTGATAGTGGTTGGCAACCAATTCCATTAACGGATGTTATAACTGCTGTTGCTGTAAAGAAAGCTTATAGAAAAGCCACTCTTTGTGTTC

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|9565633|gb|BE475142.1|BE475142
EST:     CAAGTGGAAAAGAAGGAAATTTGCGTGCATTACTTTCAACCTTGCAATAT                         ATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATT
genomic: CAAGTGGAAAAGAAGGAAATTTGCGTGCATTACTTTCAACCTTGCAATATgtaggttttt ... atcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATT
EST: gi|10255689|gb|BE823504.1|BE823504
EST:     CAAGTGGAAAAGAAGGAAATTTGCGTGCATTACTTTCAACCTTGCAATAT                         ATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATT
genomic: CAAGTGGAAAAGAAGGAAATTTGCGTGCATTACTTTCAACCTTGCAATATgtaggttttt ... atcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATT
EST: gi|14008987|gb|BG725591.1|BG725591
EST:     CAAGTGGAAAAGAAGGAAATTTGCGTGCATTACTTTCAACCTTGCAATAT                         ATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATT
genomic: CAAGTGGAAAAGAAGGAAATTTGCGTGCATTACTTTCAACCTTGCAATATgtaggttttt ... atcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgattaactagactctccatgttgttccttatctaattttttcatcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATTACTTCTGCTGCTGTAAAGAAAGCTTACAGGAAGGCCACCCTTTGTGTCC
                                      ttttttcatcttgtc  CT-rich tract
                              ttatctaattttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttaccatctctttctcccccactatttggaacatttccttatcttgattaactagactctccatgttgttccttatctaattttttcatcttgtcagATTCTTGGGCCTGATAGTGGCTGGCAGCCAATCCCACTCACAGACGTCATTACTTCTGCTGCTGTAAAGAAAGCTTACAGGAAGGCCACCCTTTGTGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - ccatctc
- - - - - - - - ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctcca