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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT

Basic information

species Glycine max
transcript GLYMA03G27460.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os11g03734.1 (Oryza sativa), 3'ss of exon 10
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggc---taaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
            | | |  | ||| |   ||  ||  ||   | | ||| ||| |  |  ||| |  |   |  || | || ||||| ||| |     |  || |||||||||||||||||||| ||||||||||  || |  |||||||||||||| |||||| |||||  || ||||   || || |||||  |     ||
-----------gttagtattcatggtttagtactt--tactttgtttaggattctagcatctgttctctctttgacaattaatgtgtaaatctaaaa-accagCTGGAACCCAGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os12g03530.1 (Oryza sativa), 3'ss of exon 13
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
 || |  |   | ||  | |  |  |    |  || | ||  |   |    ||| ||      | | | |   | |       | ||| |   | || || |||||||||||||||||||| ||||| ||||  ||||  ||||| |||||||| |||||||||||   || ||||   || || |||||  |     ||
-gttag-tacctccagctttgctccttt--ttatttccaacgttcttg---ttggtcacaagtacg-cgagtttgactagaccttaatgta-atgatcagCTGGAACCCAGATGCAATTGTGTTCAATTCCTGGCAGCAGTATGGCACTCCTAGTTATTGGGTGCAGACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 15
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
 || |  |   ||    | |    ||    |  || |||| ||   |    ||||||   |   ||  | |  |    | |     | |    | || || |||||||||||||||||||||||||| ||||  || |  ||||| |||||||| |||||| |||||  || ||||   || || |||||  |     ||
-gttag-tacctttggctttgccttttttat--tttctaacattcttc---ttgttca--caagtgcttgagtttgactagctctgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 13
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
  ||  ||   |     ||| ||  |    | |||   ||    | ||| ||   |   |    || |||   |  || ||| | ||| |   | |  || |||||||||||||| ||||| ||||||||||  || |  |||||||||||||| |||||| ||||   || ||||   || || || || || |   ||
gttagtatacat---ggtcttatactttctttgtt--caaggattctagcatctgtttcctctctgacta--ttgctaatgtataaatgtg-ataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttc--tgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
        |||   | |  |  | ||    |     |||     | |      ||| |||   |  |||    | || |||| || |       |  || ||||||||||| || || || || ||||||||||  |||| |||||||||||||||||| ||| ||||     |||||   ||||| || || || |   | 
--------gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctct--aacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttc--tgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
 || |  | || |   || |  | |||   |   ||||      | |    ||| ||   |     |||    | || |||| || |       |  || ||||||||||| || || ||||| ||||||||||  || | |||||||||||||||||| ||| ||||     |||||   ||||| || || || |   ||
-gttag-tattcttggtttt--ttttaccct--ctacttgttcttttcccgttgctctaac-----gctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 15
agtaaaatgttttcaattctaatgttaa-ggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
       | | |   | | || | | || |||  |||     |||| | ||||      |  | |     || |     |||  |   |||   |  | ||||||| ||| |||||||| || || ||||| | ||| || ||||||||||||||||||||||| |||   || ||| | ||||| || |||||||| |||
------gtatctctcactttagtttcaacggtttttatcggtatatcttgaatg--cggtaatcagaaacaagcc--cgttgcttttgttttgtttttcagGTGGATCCCTGATGCAATAGTTTTTAACTCGTCTCATCTATATGGAACTCCTAGCTATTGGGTCCAACACTTCTTCACCGAGTCAAGCGGAGCAACTCTT

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 15
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
 |||   | |     | | |   |||    |||||||| |   |  ||      |     |  || | |||| |  | |                   ||||||||||| |||||||| || |||||||||| ||| || |||||||| |||||||||||||| |||   |||||  ||||||| || |||||||| |||
-gtatc-tctcacttacttttccgttcgaatggttactcaggaagataaggcaataatctcaaattgttaaattggtttc------------------agGTGGAACCCTGATGCAATAGTCTTCAACTCCTCTCATCTATATGGAACACCTAGCTATTGGGTTCAACGGTTTTTTGCAGAGTCAAGCGGAGCAACTCTT

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
lower sequence: PP1S106_48V6.2 (Physcomitrella patens), 3'ss of exon 17
-----agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggcta-aactaatatt-gtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
        | |||  |     || |  |    |       | ||||  |     ||||  | | | |  ||  |  ||   | |||  |||   | |  | ||  || |||||||||||||||||||| |||||||| |  || |  || || || || ||||| ||||| ||    || ||   | | || |  || ||    |||
catcacacagaatagtccactttttcctccctaa------aataaagaacagtaaatttctacgcatactgagtggaagggacatttatgtgtgtgttcg-caacagATGGAACCCAGATGCAATTGTTTTCAACTCTTGGCAACAATACGGGACACCCAGCTACTGGGTTCAGCATTTCTTTAAAAACTCCAACGGTGCCGACCTT

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|51337485|gb|CO981351.1|CO981351
EST:     GTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: GTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|6134767|gb|AW133160.1|AW133160
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|19348102|gb|BM892634.1|BM892634
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCA
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCA
EST: gi|9899023|gb|BE607991.1|BE607991
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|298166525|gb|HO009964.1|HO009964
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGAGAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|9899207|gb|BE608105.1|BE608105
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|22523744|gb|BU082555.1|BU082555
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|51335508|gb|CO979374.1|CO979374
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|10710450|gb|BF010168.1|BF010168
EST:     GTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: GTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|27424547|gb|CA936067.1|CA936067
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT
                         aactaat  putative branch site (score: 2)
                                          tttctgtc  putative PPT
                       taaactaatattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA