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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 10
gtaagtaatacatctgtgacatgt-atgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
          || |||     ||| |      |      ||||  |  ||| |||          || | || ||||||          ||  | |   || ||| ||   | |||    ||||||||||||||||||||||||||||||| || || || |||||||||||||| |||||||||||||| |||||| |||| ||||||||||| ||||||||||
---------tcacctgaagattgtgacacacctgcttccatatcaattaagtagtg---------ctatactgattatga-------gggtaatttcttttttttttggcatgtgtcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACCAAACAAGATGAAGGATTTGTTTCTGGTATTCGTGGAGTAGAATGGGATG

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaa-agcagtagctctctgcctctccttat-tatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
                          || | |    ||   |     | || | || |    |   |   ||||| |||      || | |   |  |   ||||| | || |   ||      ||||||| ||||| |||||||||||||| || || ||||| || ||||||||||| |||||||| ||  | |||||||| ||| | ||  | || |||||||
-------------------------cgttactggcaattcttaatctatagaattatcctaatttgtgcacttatctataaattcataatggcttacactatcttttt-cttttcatttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 10
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaa-gcagtagctctctgcctctccttattatggtactatgaagttgt--gtaaattctttctgctgtatgttgcctgt-----agGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
                               | |  | ||||  |   |   | ||  |  ||  ||    |||   |  |  | || | || |   ||||||| || || | ||   |  || |     ||||||| ||||| |||||||||||||| || || ||||| || ||||||||||| |||||||| ||  | |||||||| ||| | ||  | || |||||||
-------------------------------tgataaaatatcaactgatataatacgttactcactagaattagcctaat-ttgtgcacttatctataaattcattatggtttacactatctttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCTCTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
                |  |||   ||  | |   | |   |   || | |  |  |   |    ||      | ||| | ||      || ||  |||  | |        | |    |  |||| || |||||||||||||||||||| || || |||||||| |||||||| ||| | ||||| ||  | || ||||| || ||     | || |||||||
----------------ttccatacttgaaactttaggtgcttttggagaactcttacatgcatggtcaatgactcatgatccttgttctttatgacaatattat--------tctgatttacagGTAGAGACTGTGTTCCATGAATTTGGCCATGCTCTTCAGCATATGCTTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATG

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
                     ||   ||||    || ||| |  | | |          |||   ||   || |    | || ||    |  ||| |  | | | |||   |||||   || ||||||| ||||| |||||||||||||| || || |||||||| |||||||| || || ||||| ||  | ||| |||| ||||| ||  | || |||||||
-------------------agtgggggtgatggtggttatgtttatacatagaatatcatcttgttcagtttgtgcatgcacaatcttatattgttagatatatatgc---atgtt--ttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
                     ||   ||||    || ||| |  | | |          |||   ||   || |    |  | ||    |  ||| |  | | | |||   |||||   || ||||||| ||||| |||||||||||||| || || |||||||| |||||||| || || ||||| ||  | ||| |||| ||||| ||  | || |||||||
-------------------agtgggggtgatggtggttatgtttatacatagaatatcatcttgttcagtttgtgcatgcgcaatcttatattgttagatatatatgc---atgtt--ttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv06s0061g01070.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
            | | |   || | |  ||    | | |     |   | || |   | | |  |||     |  ||  |   || |  || || |||||  |    |  ||        | ||||||||||||| |||||||| ||||| || ||||||||||| ||| | || || ||||||||| |  ||||| | ||   ||| ||  | ||||||||||
------------ttttttttatct-tccgagatggaacaatcatatttatcaat---tttataactcatgc-agcatatttagataatcttatgaaaattgatgtcaccata-------agcagGTTGAAACTGTCTTCCATGAGTTTGGCCATGCCCTTCAGCATATGTTAACCAAGCAAGATGAAAGTCTTGTTTCAGGTTCTCGAGGGATAGAATGGGATG

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|20300828|gb|BQ163771.1|BQ163771
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|211206211|gb|FL245890.1|FL245890
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|28909606|gb|CB331010.1|CB331010
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|67011759|gb|CO440508.1|CO440508
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|31664241|gb|CD572966.1|CD572966
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|67026706|gb|CO455455.1|CO455455
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|26456915|gb|CA828498.1|CA828498
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|67025999|gb|CO454748.1|CO454748
EST:     ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
EST: gi|15554185|gb|BI644183.1|BI644183
EST:     ATCAAACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT
genomic: ATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACT

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: 163

AGCTCGCAATGGTTTGGCTGCTAGGCTGCCTGTTGCCCATATAGTGTGCAATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

AGCTCGCAATGGTTTGGCTGCTAGGCTGCCTGTTGCCCATATAGTGTGCAATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 144

AGCTCGCAATGGTTTGGCTGCTAGGCTGCCTGTTGCCCATATAGTGTGCAATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 189

AGCTCGCAATGGTTTGGCTGCTAGGCTGCCTGTTGCCCATATAGTGTGCAATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaata ... ttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG
                         taaattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtagGTTGAAACTGTGTTCCATGAATTTGGGCACGCCCTTCAGCACATGCTTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG