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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccacataagttttcctgttagttatttttatttgtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaactatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT

Basic information

species Glycine max
transcript GLYMA19G35460.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 3'ss of exon 14
gtaccacataagttttcctgttagttattttta-tttgtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaactatttgagcggt-taaatttttctcttatt--gcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT-------
          | | ||   | |  ||| ||  | ||||  | |  ||| |   |  || |  ||  | |    ||| | |   | |  | || |||| || || ||   | | ||||| | | || ||   | ||||||||||||||||| |||||||| ||||||||||| ||| ||||   |||||   | || ||  | ||||||      |||||  ||||||    || | ||||  |       
--------gtattctttaagctgcttaattggagtttgctctttcattatgtagtttaaaattc--ttagctattgctttccgacttatattataaa-tacttaagaaatctcaatttcttttttcttttcctcctagtgcagGAGTTGATCCTCCATCCTCTCGTGATCCTCCTATCCCACTTGCTGCAACTGCTTCGGACCATCTG------TCTTTG-CAGAATTCCATATTGCTGGATTCATCCCT

upper sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 13
gtaccacataa---gttttcctgttagttatttttatttg---tacctcaattttcaggac-tagatgtcattcaatggttgatc-tgttagtgtttt---tttaaactatttgagcggttaaattttt--ctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT-------
|||     | |   | ||   ||| | ||| | |||  |     |  |    ||| |  |  ||  |     ||| ||  |||   | |||   | ||   |||  |  ||   |    | |  || ||   || | ||   ||||||||||| ||||| |||||||| ||||||||||| ||| | ||   ||| |   | || || |||||||||      || ||| ||||||  |  ||| || |  |       
gtattcttttaactgcttagttgtcaattactgttaagtaatagaaatggccttttatcatgtatttcctggtcattgactgacaatattatcatcttagttttctatgataaaaaaaatcagtttcttatttccttttaatcctagtgcagGGGTTGATCCTCCATCGTCTCGTGATCCTCCTGTTCCGCTTGCAGCAACAGCTTCAAATCATCTG------TCCTTA-CAGAATTCAGCACTGCTCGACTCATCTGT

upper sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
gtaccacataagttttcctgttagttatttttatttgtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaactatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT-------
                              |||||  |   | |    |||||    ||   ||||| ||      | | | | || |  | ||||   ||| |    |||   ||| || ||| |   ||||||||||||||||| |||||||||||||||||||| ||| | |    ||| |  || ||||| |||  |||  ||       |  |||||   |  |||  |||  |       
------------------------ggggcattattaatttattatgcatcagg----gaacacattctatt-----tttttcactgatactataaaagttttaatttctta---tttgcttttaat---cctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCA-------TTGCAGAACTCAGCACTGTTGGACTCATCCCT

upper sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaccacataagttttcctgttagttatttttattt-gtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaac-tatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT
                               ||||  ||  ||    ||     | || |  |  ||   ||     ||  |||   |    | | |  |  ||| || | |||||| |  |||| || |||||||||||||||||||||||||||| ||||||||||| ||||||| ||||| ||  || ||||| |||  ||  |||||      | | |    | | ||   | | ||
------------------------------gtattgagtttctttccttatgaaagtacagtttgtttt-tgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttcttttt-cccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT

upper sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------gtaccacataagttttcctgttagttattt---ttatttg-tacctcaattttcagg-actagatg-tcattcaatggttgatctgttagtgttttt-----ttaaactattt--gagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAAC---AGAATCAACTACTTCTGGCAT
                                        |  | || | |||  |||| | |   |     ||||   |   | | | || |   ||||  || |    |||||||  |   |    ||| |||     || ||| ||||  || ||| ||| ||||||||||||||||||||| |||||||||||||||||||||||||||||||| || || |||  |||||| || ||||| ||||| || |||| | |||  |    |||||||| | ||||| |   
gtattgaatggttttgtcaattagattattatctttgatcataatattaatttgactgtcaatctatgaagctattcaatggtttactgttgaatcactatctgattgaccaatggtcaaaacgaagctgtctttaatgtttgaacaatttatgaacggctaagtttttctcttattgcccctagcgcagGAGTTGACCCTCCATCATCTCGTGATCCTCCATTTCCTCTTGCTGTTCCAGCATCAAATCAACTTACAAACACTTCGATGGTAGAATCAAATGCTTCTAG---

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|18041114|gb|BM309408.1|BM309408
EST:     GTCTGATAAGCATAATTCATCTTCTCTCCGGTCAACAAGTTTGGATCTAG                         GAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCG
genomic: GTCTGATAAGCATAATTCATCTTCTCTCCGGTCAACAAGTTTGGATCTAGgtaccacata ... cctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttttaaactatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT
                             tttttctcttattgcc  CT-rich tract
                        ttaaatttttctctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccacataagttttcctgttagttatttttatttgtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaactatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT