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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT

Basic information

species Zea mays
transcript GRMZM2G054247_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 3'ss of exon 2
----------gtgcctgcttcagtagagatgctactcctttgcctt--gtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
            |  | | ||| | | | |     |  ||||  |   |||  |    |   ||     |   |   |   ||||| |  | |||| || ||| | || ||||||||||||||||||||||| || ||||| |||||||||||  |||||||||| |||||||||||||| || |||       
gtgagtggagagggattcctcacttgggctcaattttgtttgattcgagtggataatcgtgcttagttgttcctcccttgctgttgcgtcgcagCTTGTCGTGGTGTATGTGGATTTCAAGCTCGACGAGAGCTATACGCCTAGCAAGATCTCTGTCCGGGCCGGCGATGGCTTCCACAATCTCAAG-------

upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G25220.1 (Glycine max), 3'ss of exon 2
gtgcctgcttc---agtagagatgctactcctt------------tgccttgtg---attcgatggttttgagactaattggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
  ||||| ||    ||  |||||  || || ||            | | | ||    ||| |||   | |  ||  ||     |   | |||| | || || |  ||||||| ||||||||||||||||| |||||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||       
-agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG-------

upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G13520.1 (Glycine max), 3'ss of exon 1
----gtgcctgcttcagtagag----atgctactcctttgccttgtgattcgatggttttgagactaattg---------gttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
    || | |     | ||  |    ||  |   |  ||| ||    ||   |  || |  | |  |||||         |||  || |||| | || || |  ||||||| ||||| | ||||||||| |||||||||||||||| ||||||  | |||||||  ||||| ||||| || |||||| | |||       
gaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaaagtatcaataagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTACGTCGTTTTCAAGCTTGACGAGAGTTACACGCTGAGCAAAGTTTCCATCCATGCCGGTGATGGTTTTCACAACTTGAAG-------

upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G20840.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------gtgcctgcttcagtagag----atgctactcctttgccttgtgattcga---tggttttgagact--aatt---ggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
                                                                      || | |     | ||  |    ||  |   |  ||| ||    ||   |   || | |    | |  |||    ||||  || |||| | || || |  ||||||| || |||| ||||||||| |||||||||||||||||||||||  | |||||||  ||||| ||||| || |||||| | ||||||   |
gtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT

upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G06190.3 (Glycine max), 3'ss of exon 3
gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
        | |  |  | ||   |     |    ||    ||      | || |   |  ||  ||    ||||||  | || |  ||||||| ||||||||||||||||| || ||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||       
-------gtacgttgtaaataa-ataaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtg--gcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG-------

upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G09250.1 (Glycine max), 3'ss of exon 1
----gtgcctgcttcagtagag----atgctactcctttgccttgtgattcgatggttttgagactaattg---------gttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
    || | |     | ||  |    ||  |   |  ||| ||    ||   |  || |  | |  |||||         |||  || |||| | ||||| |  ||||||| ||||||| ||||||||| ||||||||||||| |||||||||  | |||||||  ||| | ||||| || |||||| | |||       
gaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaaagtatcaataagaattgtaatgtggggtttcattttgttgtggtagTTGATTGTGCTTTACGTGGTTTTCAAGCTTGACGAGAGTTACATGCCGAGCAAAGTTTCCATCCTTGCCCGTGATGGTTTTCACAACTTGAAG-------

upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
--gtgcctgcttcagtagagatgctactcctttg---ccttgtgattcgatggttttga-gactaattggttctatg--ttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
  |||  |||     | |   |   | |  |||    ||   | ||    ||||||||  |||| | ||||     |  || |     |||| |||||  | || |||||||||||||| |||||||| ||||||||||| |||||||| || || ||||| ||||||||||||||| | |||       
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG-------

upper sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
lower sequence: PP1S42_273V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
                     |   ||   || | |    | ||||| |  |   |  |  | |   |   | |  ||   | || || ||  ||   | |||  |||| ||| | ||||||||||||| |||| ||||||||||| |||| |||||| || || || || ||  ||   || ||  | ||   |       
gtttgatcagatgttaggttttagatggagcattgggagagttactcatg-gttgtaagtatagtcagccctcattctttctcgtcctctgacgt-ttgcagCAAGTTGCGCTTTTCGTGGATTTCAAGGTCGATGAGAGTTACACCCCGAACAAGATATCAATTCGAGCTGGCAATTCTTTTCATGATCTTCGG-------

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|12045796|gb|BF727935.1|BF727935
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|91873254|gb|EB403211.1|EB403211
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|89252141|gb|DY623927.1|DY623927
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGA
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGA
EST: gi|71432068|gb|DR813118.1|DR813118
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|149073064|gb|EE161334.2|EE161334
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71427966|gb|DR809016.1|DR809016
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|78180912|gb|DV551285.1|DV551285
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71297610|gb|DR784754.1|DR784754
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCTG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 22

GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 39

GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 23

GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
                           gactaat  putative branch site (score: 23)
                            actaatt  TA-rich tract