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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttactttcaaaacgtgtatcagccttttgaattgtttgtttcagatgccatttttatttttgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC

Basic information

species Glycine max
transcript GLYMA19G37570.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
gtaagtttactttcaaaacgtgtatcagccttttgaattgtttgtttcagatgccatttttatttttgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
||||||| |  ||   | |||   |     || |  ||| |||  ||||| |   | |  |  |  |   || |   ||  |     | |||||||    ||||||||||||||| ||||||||| | || || |||||||| ||||||||||| ||||| |||||||||||||| ||| | |||||| ||   |||||||
gtaagttcatatt---accgttacttttatttgttgatttttt--ttcagcta--aatcgtgctagt---aagtgctttcgatgtaatattctcta----gCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 13
gtaagtttactttcaaaacgt---gtatcagccttttgaattgtttgtttcagatgccatt-tttatttttg-caaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
||||||    |||| |  | |      |   || ||  |    ||| |    ||    ||| || || |||| |  ||   |||    | |  |||   || |||||| || |||||||| || ||||| || || || || |||||||||||||| || ||||| ||||| |||||||| ||| | |||||  |    ||| |||
gtaagtaccatttccattcttcagaagttcacccttcaatccctttttcattgaaaatattattcatctttggcttatcttgttctttttccatttaaata-ttagCCCGAATGGATGGCACCTGAAGTGCTCCGAGATGAACCATCCAATGAGAAATCTGATGTCTACAGTTTTGGTGTAATCCTATGGGAACTTATGACAATGC

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
gtaagtttactttcaaaacgtgtatcagccttttgaattgtttgtttcagatgccatttttatttttgcaaattaagttgaactcctttttct-ctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
              ||    | |     | ||| |  |  |||||||       || || ||| |        |||||   | ||  |    | |||  ||||||||||||||||| ||||||||||| || |||||||| || ||||||||||| |||||||||||||| ||||| ||||| |||||| |    |||||||
------------gtaagttatattgttccgtttagtgtattttgttttgttacgcaattctatgt-----ggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G036902_T01 (Zea mays), 3'ss of exon 1
gtaagtttactttcaaaacgtgtatcagccttttgaattgtttgtttcagatgccatttttatttttgcaaattaagttgaactcctttttctctac-ttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
                     |||  ||||| || || | |||   | |  | ||  ||| | |            ||  ||  |  | || |  |  | ||||||| |||||||| || ||||| ||||| || || |||||||||||||| || ||||| || ||||| ||||| ||| | |||||  |    ||| |||
---------------------gtaagagcctcttcaacttttt---ttaagttcccctttcactgaaatttgccttgtataatcctgtcttttaaatatcagCCTGAATGGATGGCACCTGAAGTGCTTCGAGATGAACCATCCAATGAGAAATCTGATGTCTATAGCTTCGGTGTTATCCTATGGGAACTAATGACACTGC

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtttacttt---caaaacgtgtatcagccttttgaattg--tttgtttcagatgccatttttatttttgcaaattaagttga-actcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
||||||| | |||     ||||    |   ||      |  |   ||| ||  || | | ||||  |    || ||  ||| |    |||   |||  | || | |||| ||||||||||| |||||||| || || || ||||| || ||||| ||||||||||| |||||||| || ||||||||||||||| | || |||||||
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctatttcca---atggaagctaaataattactgactttgatata-tcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtttactttcaaaacgtgtatcagcct--tttgaattgtttgt-ttcagatgccat---ttttatttttgcaaat-taagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
||||||||  |   ||      || || |    | | | ||  |||| || || ||  ||   |  | || |  ||||| |||  |  ||   |||   |  | | |||||||||||||||| |||||||||||||| || ||| |||| ||||| ||||||||  | || ||||||||| | |||||||||||  | ||||||||||
gtaagttt--tactaagctagatagcaacacaatctcagttccttgtatttaggtgatatggatcattttgtcacaaatataaaatttacatttttcatttca-tcagCCTGAGTGGATGGCACCAGAAGTTCTTCGGGATGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGC

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|298178752|gb|HO024487.1|HO024487
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
EST: gi|193708650|gb|FK644986.1|FK644986
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCCCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
EST: gi|207832729|gb|GD803545.1|GD803545
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGGTGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
EST: gi|8285414|gb|BE022973.1|BE022973
EST:     CTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
EST: gi|193428872|gb|FK397586.1|FK397586
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
EST: gi|208336673|gb|GE135105.1|GE135105
EST:     AGTCAGCNGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: AGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
EST: gi|193720882|gb|FK659046.1|FK659046
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGT
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGT
EST: gi|207780259|gb|GD752628.1|GD752628
EST:     CCCG-CTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
EST: gi|208280179|gb|GE075477.1|GE075477
EST:     CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACT                         CCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG
genomic: CCCGACTAAAGGCAAATACATTTCTCTCATCCAAGTCAGCTGCTGGGACTgtaagtttac ... ctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatgccatttttatttttgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
                                    ctcctttttctctact  CT-rich tract
         atttttatttttgcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttactttcaaaacgtgtatcagccttttgaattgtttgtttcagatgccatttttatttttgcaaattaagttgaactcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC