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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcatttctttctatttagcagtagtgtatgtacatcagattaacatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG

Basic information

species Glycine max
transcript GLYMA01G00870.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
------------gtctgcatttctttctatttagcagtagtgtatgtacatcagatta-acatctctctgaatt--tcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
            || ||||  | | |  || ||||  |  ||  ||  |||    | |      | | |  |||   ||||| ||||| ||||||||||||||||| ||||||||||||| ||  || ||  ||
gtaaatgcggttgtttgcacctatgtg-atatagctcttctgattggtcattgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 6
--------gtctgcatttctttctatttagcagtagtgtatgtacatcaga--ttaac--atctctctgaat------ttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
        |  ||||  | ||  |||    ||  | | |    |    |||  || ||  || |    ||        | ||||| ||||| |||||||||||||||||||||||||| |||| ||  || ||  ||
gtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTCAAG

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 6
--------------gtctgcatttctttctatttagca-gtagtgtatgtacatcagattaacatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
               |  |  |||||||  ||    |   |  || | ||  |  | ||   | ||| |   |  |  |||| |  || || |||||||||||||||||||||||||||| ||  ||||   ||
gtatgtgcttgctgattagtgtttctttgcataacccttattttggaggttgagtaaatgttcttctttaccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------------------gtctgcatttctttctatttagcag-------tagtgtatgtacatcagattaacatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
                                                        | || ||||  | |   |  |||         | || ||| || | ||||| | | || | |  || ||||||||| ||||||||||| ||||||||||| || || |||||||  |||||||||
gtctgtagacaatactatttcttgtccaagttatctgagtcacactttcggagttttgtgtatttgctacacctgggcacacctcttcaatgcatggacgttagatttatagctttgttgatctcagGTTTACATAATTGGAGGTGATGGAACTCAAAAAGGGGCATCTGTGATTTTTGAG

upper sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------gtctgcatttctt--tctatttagcagtagtgtatgtacatcagat----taacatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
                              | ||   |  | |  || |  | | | |  |     |||| |  |     | ||||   | |||  ||||||| ||||| |||||||||||||| |||||||| || ||   ||| ||    |||
tgaagatcgcttcaaaacttttcgatgccggcctcagtcacctcatcaacctcgtattttttgcaatacagctcaccctgtgacattgatttga-cttcagGTCTATATCATTGGAGGAGATGGCACTCAGAAAGGAGCTAATGCTATCCACGAG

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|7691740|gb|AW759862.1|AW759862
EST:     ATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAG                         GTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTT
genomic: ATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtctgcattt ... tgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTT
EST: gi|10237267|gb|BE806155.1|BE806155
EST:     ATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAG                         GTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTT
genomic: ATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtctgcattt ... tgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTT
EST: gi|208272742|gb|GE066234.1|GE066234
EST:     ATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAG                         GTTTATATAATTGGAGGAGATGGAACTCAGAAGG
genomic: ATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtctgcattt ... tgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctatttagcagtagtgtatgtacatcagattaacatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
                               gattaac  putative branch site (score: 2)
                                     catctctct  CT-rich tract
                                attaacat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcatttctttctatttagcagtagtgtatgtacatcagattaacatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA