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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

Basic information

species Glycine max
transcript GLYMA15G10030.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 16
gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
           || |  || | ||     || ||  |  ||||        |  | || ||  |  ||  ||||   |     |||| || | |   |||||||| || ||||| || ||| | ||  | |||||||| || || ||||| || ||||||||||| ||||||||||||| ||  ||||| || || ||||
---------gttagacatgttttcaacgcatgcattccattttgcgcac--tccacaattt--tgatatcttaaaatatatcgttttcttttcttt-cagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA

upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattga---taagttaatactaatttaaggaagtgaattttt---ttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
      || |   | | ||| |   || | |  ||| || |          ||||   | |   || | |   || |  ||     |||||   |||    ||||||| |||||||||||||| |||||||| |||||||||||||| |||||||| || ||||||||||| || ||| | ||||| |||||||| || |||||||
------tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA

upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------------------------------------------------------------gttgtgtacaatacaagtgatc-tcttttgataca------gactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtg---tgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                                                                         || | |   ||     |   | ||  | ||||        |  | |||  | |||   | |||| |   |  || |||   ||    |||   |   ||   |   ||||| ||||||||||| |||||||||||  ||||||| || || || |||||||| ||  ||||||||||||| || |||||   |||||||||||||||||
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA

upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S70_181V6.1 (Physcomitrella patens), 3'ss of exon 15
-----------------------------------gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattg-ataagttaatactaatttaaggaagtgaatttttttg-tgtgaa----cagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                                    | |  | || | |      ||     ||||    | || | |   |   |||   ||  | ||   |  |||  |    | ||    | || ||| ||    ||||| ||||||||||| ||||||||||||||||||||||| ||||| ||| |||||||| ||||||| || || || |||||   ||| ||||| || ||||
gtgaatatttcatacctcgaattattatccagaatttcggattcacttctgcaagtcatcgatgatgtgtagtgctgttattgaaattctgtatttcaagtgttttttttgttgttaaacgcatgtgatgttaaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTGATTGACCGGGAGTACCTTGAAAGGGACAAAGCCAATCCTCAGATCTACA

upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S143_152V6.1 (Physcomitrella patens), 3'ss of exon 15
--------------------gttgtg-tacaatacaagtgatct-cttttg-atacagactgttttctctctgattgataagttaatactaatttaaggaagtgaat-----------ttttttgtg--tgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                     || || |  |  |    || | | ||| || | | | |   |  | |   | || | |  |  ||| |  |||| |  || |   |           ||| ||||   |   ||||||||||||||||| ||||||| ||| |||||||| || ||||| || ||||||||| |||||||||| || || |||||   ||| ||||| || ||||
gtgaggatttcattcctggaattatgatttagaatctttggtttacttgtgcaaataaatgataatgtaaataatcgctgtgaaaatgccgatttcaaaaactttgtcgtccaacgcatttgttgttacttcgcagCTCAAATTTCCAATCAAACCAGTTGATTTGAAGAAGAGAATCGAGAGTCTGATTGACCGGGAGTATCTTGAAAGGGACAAAGCCAATCCTCAGATTTACA

upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 16
gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                              ||  | |||  | || |  || ||    |   |  ||  | || |        ||||| ||||||| |||||||| || || ||||| ||||| |||||||||||| | ||||| |||||||| ||| | |||||  ||||| |||||||||||||||||||  ||||||
-----------------------------gtaaggcctggctgctgttggaatgtggtgccgacgctg-tatatgt-------tttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 16
gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                              ||  | |||  | || |  || ||    |   |  ||       |||  ||  ||||| ||||||| |||||||| || || ||||| ||||| |||||||||||| | ||||| |||||||| ||| | |||||  ||||| |||||||||||||||||||  ||||||
-----------------------------gtaaggcctggctgctgttggaatgtggtgccgacgct-------ggatatgt-tttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

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|22523750|gb|BU082561.1|BU082561
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|19934696|gb|BQ079726.1|BQ079726
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAAGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|11687833|gb|BF595509.1|BF595509
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|6725094|gb|AW309493.1|AW309493
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|18734880|gb|BM528438.1|BM528438
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|208127538|gb|GD923940.1|GD923940
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|58020712|gb|CX707454.1|CX707454
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAATCCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|151404598|gb|EV274412.1|EV274412
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCA-CAG                         CTCAAATTTCCA
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCA
EST: gi|15812462|gb|BI784737.1|BI784737
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|209706055|gb|BW680825.1|BW680825
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|15814238|gb|BI786513.1|BI786513
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|209700820|gb|BW661251.1|BW661251
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|11687834|gb|BF595510.1|BF595510
EST:     CTATGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATGAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|6567265|gb|AW234876.1|AW234876
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAGAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|58020885|gb|CX707627.1|CX707627
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAATCCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|9902981|gb|BE611949.1|BE611949
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|9902896|gb|BE611864.1|BE611864
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|17401651|gb|BM178433.1|BM178433
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|58020543|gb|CX707285.1|CX707285
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAATCCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|15204199|gb|BI426967.1|BI426967
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|17400275|gb|BM177057.1|BM177057
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATC
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... gtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgattgataagttaatactaatttaaggaagtgaatttttttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                  tactaat  putative branch site (score: 1)
                                      tttttttgt  putative PPT
     attgataagttaatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- tgtgtac
- - - - - - -caagtga