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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagaagtatcaagtcacagaaacaacttgctattgattggtgttttgtgcgtacatggattattactcattctgctctgtacgtttcatcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTCG

Basic information

species Glycine max
transcript GLYMA05G01980.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G01980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g07960.t01 (Vitis vinifera), 3'ss of exon 5
cttagaagtatcaagtcacagaaacaacttgctattgattggtgttttgt--gcgtacatgg---attattactcattctgctctgtacgtttc-atcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTCG
        | |||  |   |  |     || | |||  |   | |||| |    |||  |||    |     || |    | |   ||  |||  || | |||||| || || ||||||||||||||||||||||||||||| |||||||||||||| |
------gctgtcagatttgacgactttgtttccatttttaattttttttttgaagtagttggcaagtcccagctaaactggttgcatatttttttatgaactgcagGTCAGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTG

upper sequence: GLYMA05G01980.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 3
------cttagaagtatcaagtcacagaaacaacttgctattgattggtgttttgtgcgtacatggattattactcattctgctctgtacgtttcatcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTCG
      ||  | | | ||  ||   |  |  ||||||    | ||       | | |      ||    | | |       | ||  ||  || | |    ||||| || || |||||||||||||||||||| || ||  |||||||||| |||||||
agtatcctatgcactttcttgttctatgagtaacttggctgtaatca-----tggcgtacgtgtgatacagtgcgtgagacgttcgttat-ttgcgttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG
















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|298181365|gb|HO022804.1|HO022804
EST:     CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|298191054|gb|HO038533.1|HO038533
EST:     CCTTCTGTTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|298184467|gb|HO029680.1|HO029680
EST:     CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|10232163|gb|BE801051.1|BE801051
EST:     CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|12687894|gb|BG154290.1|BG154290
EST:     CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|58025024|gb|CX711765.1|CX711765
EST:     CTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CTTCTATTGGCTTCGTGAACAAAATTTTCCACCC-AAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|151411773|gb|EV281584.1|EV281584
EST:     CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|298185117|gb|HO030330.1|HO030330
EST:     CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
EST: gi|18721187|gb|BM523328.1|BM523328
EST:     CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCT                         ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT
genomic: CCTTCTATTGGCTTCGTGAACAAAATTTTCCACCCAAATGTTGATGAGCTgtgagcactt ... tcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgcgtacatggattattactcattctgctctgtacgtttcatcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTCG
                                        tttcatc  CT-rich tract
               attattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttagaagtatcaagtcacagaaacaacttgctattgattggtgttttgtgcgtacatggattattactcattctgctctgtacgtttcatcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - -caagtca
- - - - - - - - - - gaaacaac
- - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - -attggtg
- - - - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catggat