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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

Basic information

species Zea mays
transcript GRMZM2G151549_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 2
caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttg--tttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
     || ||  |         |  | | |   ||||     | |   || || ||  || | | ||     | |    || |  ||  | | |  |  ||||| |||||||  ||||| |||||  |||| || ||||||||||| |||||||||||||| |||||||| || |||||||| || ||||| |||||  | |
-ctgttttagtggttttaaaagaattattctacttttggaagtttgaatt-ttgtggtatgagtcctgtctgactatgtaaacaatgattctgctgaaacagATTGGTCCTGCACAGATAGAAGCGTTGTACCAATATGCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAGTACAGAG

upper sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttg--tttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
     |  |  | | | |||  |   |     |  |  ||   | |  |||  || ||    ||   | |  | ||   ||     |  | | |     ||||| |||||||  ||||| |||||  |||| || ||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||| || ||  | |
--tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG

upper sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
--caaaattcagatgaa-acgttga--agctgtgc---attttttattgctatagcttgttttgtgataaatgcta-atgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
      |||  |||||  | ||||   |  | ||    || || |   | | | | ||  ||||||     ||  | |  |||     |   |||| |  |  || ||||| ||||| ||||||||||| ||| |||| ||||| ||||| ||||||||||| ||||| ||||| || || ||||||||||| |||||||||||  |  
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA

upper sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 2
-caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtg-ataaatgctaatgaattg-atcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
 |    ||  | ||     |||  |||    ||||   |    | ||| || ||  ||  ||      ||   ||||  |||  |  ||  ||  |    ||||| || |  || ||||| || ||  | |||||||||||||||||||||||||| ||||| |||||||| || |||||||||||||| || |||||  | |
tcctgtttttgttgttgtattgttgcta---atttgacagaattctaggtttttgggtctatttggcttacaaaattatatcccttttttcttttctgaccagATTGGCCAGGAGCAGATAGAGGCATTATATCAGTATGCCAAATTTCAGTTTGAATGTGGAAACTACTCTGGTGCTGCTGATTACCTGTATCAGTACAGGG

upper sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
--caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
  | |    |  |||| |        |  ||| ||      ||||      |||    |   |  |   | |  || |    |   ||  ||  |  || |||||||| |||| || ||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| ||  |||| ||||| || ||||||||  
atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggtctgactacatcgtatgaa--tttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA

upper sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
--caaaattcagatgaaacgttgaagctgtgcatttt-ttattgctata-gcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
     |||  |  |   |  | | |  |   | | ||  ||   |  |  |  ||     | |||| |   |  |  | |   ||    || ||     || |||||||| |||| || || || |||||||||||||||||||| || ||||||||||| || |||||||| || ||  | || ||||| ||  ||||||| |
attgtaat--atgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtt--tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG

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|148947189|gb|EC892527.2|EC892527
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|148988254|gb|EE031628.2|EE031628
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|29946193|gb|CB816026.1|CB816026
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|149086591|gb|EE176135.2|EE176135
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|148945927|gb|EC891220.2|EC891220
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|71772604|gb|DR970532.1|DR970532
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|211543296|gb|FL204964.1|FL204964
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|148932020|gb|EC875324.2|EC875324
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|31406351|gb|CD485083.1|CD485083
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|211543294|gb|FL204962.1|FL204962
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATTGGTCCTGA
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGA
EST: gi|148942799|gb|EC887829.2|EC887829
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|211543298|gb|FL204966.1|FL204966
EST:     CAGGCC-GACAAACAGTACAACATCCACATGCTCCAGGAAGCGAYACCAG                         ATCGGTCCTGACCAGA
genomic: CAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGA-GCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGA
EST: gi|211543297|gb|FL204965.1|FL204965
EST:     CAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATTACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTT
genomic: CAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGAT-ACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTT
EST: gi|211543292|gb|FL204960.1|FL204960
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGC-AAATTTCAG
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 268

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGTTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 230

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGTTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 194

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGTTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 223

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGTTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGCGATACCAGgttcgggttc ... accaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
                     taatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT