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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctgacataacattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

Basic information

species Glycine max
transcript GLYMA09G06860.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctgacataacattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
                 | | | || ||| ||         ||     |||  | | | | |  ||   ||  | | | |    ||   |  |||  |||||| |||||||  ||||| ||| |||| |||||  | ||||||||  |||||||||| || |||||||||||||||||||| || || ||||| |
-----------------gtttgccaccttgaatctcacttgttctgcttttactgtgtcaattggtacctt-acagtcttggtgtttg-tatcagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 6
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctgacataacatt---caat-gccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
|| ||| || | |    |    ||||  |    ||| |       ||       |   || |||  || ||   || | ||   ||   |||     ||   |||||||||||||  ||||| ||| |||| |||||  |||| |||||  ||||||| || || || ||||||||||||||||| || |||||||| |
gtatgtttgctcttgtaggctttcattgtgttgtatatatgccattta------cagctaatcaaattcttatttggcctattgttggtcaaccattagGGCTTGGGGAAGCATGACATCATCTGCATTGAGGATCTTGTCCACGAGATCATGACTGTCGGTCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCCT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094051_T05 (Zea mays), 3'ss of exon 5
gtctgtctggtgtaccggctagtcatctttaaatatctccat--tgcttgtttgttctattactcagttttttcgctgacataacattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
    || || |  ||  |  | ||  | |    |  ||   |  || || | | |   | |   ||   |  || |   | |    |    |  |||   ||||| |||||    ||||| ||| |||| |||||  | || |||||  |||||||||| || || ||||||||||||||||| || |||||||| |
----gtttg-taaacttggaactctacatctggttcctgtgttctgtttatatatgacaatttacatgatgatctccaccttttggtgttctatcagGGCTTGGGCAAGCACAACATCATCTGCATTGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 6
gtctgt--ctggtgtaccggctagtcatctttaaatatctccattgct-tgtttgttctattactcagttttttcgctgacata-acattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
|| ||      || |  | |    || |  ||   ||  |   ||    | |    | ||  |||||    ||   ||  |||| | |  |||   ||| || | || |||||||| |||||||||  ||| ||| ||||||| |||||  | || || ||||||||||||||||| |||||||| || || ||||| |
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcagGCTCTTGGAAAGCATGGTATCATTTGCACTGAGGATTTGATCCACGAGATTCTAACAGTAGGACCTCATTTCAAGGAAGCCAACAACTTCCTTTGGCCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
gtctgt--ctggtgtaccggctagtcatctttaaatatctccattgct-tgtttgttctattactcagttttttcgctgacata-acattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT-------------------------------------------------------------------------------
|| ||      || |  | |    || |  ||   ||  |   ||    | |    | ||  |||||    ||   ||  |||| | |  |||   ||| || | || |||||||| |||||||||  ||| ||| ||||||| |||||  | || || ||||||||||||||||| |||||||| || || ||||| |                                                                               
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------------------------------gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctg-----acataacattcaatgccagACT-----TTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
                                                                                               | |      |||       | |     | | | || |  ||||    ||      |  ||||  | | ||| ||      ||||| | ||   ||    |        | || |||||||| ||||| |||||||| |||||||||||||||||  |||| ||||| || ||||||||||| ||||| || ||| ||||||| |
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 5
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgt--tctattactcagttttttcgctgacataacatt-caatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
                |  |     || ||   |||||   ||   | |  |   |   || ||   | || | ||| || |    ||   |||  || |||||||||||  ||| || |||||| | |||||||| || ||||||||  ||||||||||||||||||| |||||||||||||| || || ||||| |
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgt--tctattactcagttttttcgctgacataacatt-caatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
                |  |     || ||   |||||   ||   | |  |   |   || ||   | || | ||| || |    ||   |||  || |||||||||||  ||| || |||||| | |||||||| || ||||||||  ||||||||||||||||||| |||||||||||||| || || ||||| |
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctgacataacatt-caatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
        | | |   | |  || |||||    | | |  |  | ||||||| | |||         || | ||| || |    ||   |||  || |||||||||||  |||||| |||||| | |||||||| || ||||| ||  ||||||||||||||||||| |||||||||||||| || || || || |
--------gtttttatgtcctgt-atcttggttttttttgagggattgtttgctatatc--------ttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 6
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctgacat---aacattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
    || || ||||  || ||   | | || | ||| | |  ||  |     | |||| |    | |||| |  ||||||      ||   ||  ||| ||||||| |||  ||| ||||||||| |||||||||| |||||||||||  |||||||||| || || ||||||||||| ||||| || |||||||| |
----gtttgttgta--ggttaaataacattta-tatgttcgatgtat-----tgctataaactggctttt-caatgacattttggtatgttattgcagGCTTTGGGCAAGTTTGGAATCATTTGCATTGAAGATCTCATCCATGAGATTATGACTGTTGGGCCACACTTCAAGGAGGCAAACAACTTCCTGTGGCCAT

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
--gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctat-tactcagttttttcgctgacataacattcaatgc---cagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
  || |   | |       || |  ||  |  || ||     |      || | | || |  | | | ||     | ||| ||    || | |      || |  | || |||   || ||||| ||  |||| ||||| || |||||||| || |||||||||||||| |||||||| |||||||| ||| | ||| |||
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatga-attctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT

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|192302637|gb|FG994889.1|FG994889
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTTTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|193691684|gb|FK628905.1|FK628905
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGAT
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGAT
EST: gi|7285803|gb|AW598290.1|AW598290
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACGACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|19345954|gb|BM890834.1|BM890834
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|192302636|gb|FG994888.1|FG994888
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|209706673|gb|BW676169.1|BW676169
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|192307308|gb|FK001266.1|FK001266
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATCTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|151407003|gb|EV276818.1|EV276818
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|18732369|gb|BM527007.1|BM527007
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|24205580|gb|BU964833.1|BU964833
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
EST: gi|151401089|gb|EV270903.1|EV270903
EST:     AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAG                         ACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA
genomic: AAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAACAGgtctgtctgg ... tcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcttgtttgttctattactcagttttttcgctgacataacattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
                                    acataac  putative branch site (score: 3)
            ttctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctgacataacattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG