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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC

Basic information

species Zea mays
transcript GRMZM2G065237_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g35090.1 (Oryza sativa), 3'ss of exon 2
tccaaatttatttgccccttaaactatggattccttgttat-acattcatctgcgttatgttcatacg-atttctgttagtttgatgtat-ttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
      | |   ||    | |    |  | |  | ||  |  |   |||         || |  || |   |  | |||  ||| |||||  || || ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||
---cgctgttggtgtatgtcagtacagcgttcgcatgccaagaggctcaaactgaaagtgattgtaggtgctggttttaacttggtgtatgctgttgttgcagAGGGAGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCGAACCTGCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 2
--tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttg-atgtatt-tgctgc--tgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
     ||    || || |  | |  ||||    | |   | ||  | | |   |  |  ||||  |    | |   || |||||  || ||| || |||     |||||| ||  |||| |||||||||||||||||  |||| || ||||| ||||| |||||||| ||||| ||||| |||||||||||||||||||| |||||
ataataagaccatatgtct-tcatcctat----ttcgactgatgaact-agaaggatattgtttctcatttcttcatttgtttgtgtgcattgtggtgcatcatagAGGGGGTTTTGTACGCCAAGAAGGACTACAATTTGGCAAAACACCCACAGATTGATGTGCCAAACCTTCAGGTCATCAAGCTCATGCAGAGCTTCAAGTC

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G02070.1 (Glycine max), 3'ss of exon 2
tccaaatttatttgccccttaaactatggattccttgttat-acattcatctgcgttatgt-tcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
          |  |  ||||| | |     ||| |||   | || |     ||    |||  || |||   |||| ||   || ||||       | ||||||||| ||    | ||| |||||||||| |||  |||||||||||||  |||| || ||||| || || |||||||| ||||| |||||||| || |||||
---------gtaggtgccttagaat-----ttcattggggttacgtctcgttgaagaatgaatcttac--cttcttttttcttaatgt------cggtgcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATTTGGCGAAGCACCCTGAGATTGACGTGCCGAATCTGCAGGTGATTAAGCTGATGCAGAGTTTCAAGTC

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC--------------------
             | || |||    |        ||||| |    || | ||| |||   |  |   |    ||| || |   ||| |||| |    ||||||| ||    | ||| |||||||||| ||| ||||| ||||||||  |||| |||||||| || || |||||||| ||||| ||||||||||| || ||                    
-------------gtccgttagttaaca------ttgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgat---tcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G02410.2 (Glycine max), 3'ss of exon 2
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
             | || |||    |        ||||| |    || | ||| |||   |  |   |    ||| || |   ||| |||| |    ||||||| ||    | ||| |||||||||| ||| ||||| ||||||||  |||| |||||||| || || |||||||| ||||| ||||||||||| || ||
-------------gtccgttagttaaca------ttgttgtctcctcttgtgctttacagttgtgttaaaattgtaaggtgtgtgtgtttgat---tcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G43110.1 (Glycine max), 3'ss of exon 2
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgct-gctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
                              | | ||  |  |||||        || || |  |||| ||    |||  |||     | || | | | ||||||| ||    | ||| |||||||||| ||| ||||||||||||||| |||| |||||||| || || |||||||| ||||| ||||||||||| || ||
-----------------------------gtccgttagttaacattgtctcctcttgtgctt-tacggttgtgtttaaattgtaacgtgtgtttgattcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCGAAGCACCCGGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0050g01160.t01 (Vitis vinifera), 3'ss of exon 2
-tccaaatttatttgccc-cttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgc-tgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
  ||   || ||| |    | | | ||||   ||  | |  | | |      ||  | |||||    | ||||||  || | |||| | ||   ||  ||||||||| ||    ||||| |||||||||||||| || || || |||||  | || ||||| || || || |||||||| ||| | |||||||||||||||||
caccgttttcattagttttcctcatctatattttattagcaacaaaac--gttggatcatgtttcatctatttcttata-tgtgatattttgcatgtgtgcagAGGGAGTTTGCTATGCAAAGAAGGACTACAATCTTGCAAAACACCCCGAAATTGATGTTCCAAATCTGCAGGTGATTAAGTTGATGCAGAGCTTTAAGTC

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP00807 (Chlamydomonas reinhardtii), 3'ss of exon 1
-------------------------------------------------------------tccaaatttatt--tgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttga-----tgtatttgctgct-------gcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATC---GATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
                                                              ||     ||     ||   |      |  |  | |        | ||| || ||   |  || ||        |||  | ||       ||||||||||  |       |||||||| || ||  | ||  ||||||||| ||||||   | |||||||| |||||   |  ||||||||||| ||||| || ||||||||||||||||| ||   
gtgagcatcagttggtatgcgacctcggtgttcgcgttctttgaggcccggggacatggacgccgggcctagcgacgcttgtcggcgcacagcctgcggcgcgcgctttcttcggccgcaaatttatttccccaatgtatgcttacacacctgtatttgctcgttgtgcgcgcagAGGGTGTCCTTCAGGCGGAGAAGGACTTCAACCTCAAGGAGCACCCGGAGATCCCCGGCGTGCCCAACCTGCAGGTCATTAAGCTCATGCAGAGCTTCAA---

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29946 (Selaginella moellendorffii), 3'ss of exon 1
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
             |       | ||| |  |  | ||     |   |     ||   |  | || |||  | | |       || | || |     ||||||||||| || || ||||||||||||||||| ||  | ||||||||| |||||||||| ||||| ||||||||||||||||||||||||||||| |||||
-------------gtgaggggatcta-gcttctcctggcgcgctcgcgctcacgcatttctaatccgagatttctc--cccaat-tgttcggc---gcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

upper sequence: GRMZM2G065237_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25099 (Selaginella moellendorffii), 3'ss of exon 1
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
                         | ||  ||    |    ||||  ||  | || |  | || |||  | | |       || | || |     ||||||||||| || || ||||||||||||||||| ||  | ||||||||| |||||||||| ||||| ||||||||||||||||||||||||||||| |||||
----------------------gtgaggggatctagctcgcgcatttctcc-cttttttctaatccgagatttctc--cccaat-tgttcggc---gcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

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|87151684|gb|DY396473.1|DY396473
EST:     GCAATGAGATCTGCAAGTACCTCTTCAAGG                         AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
genomic: GCAATGAGATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
EST: gi|32798534|gb|CD950770.1|CD950770
EST:     GATCCGCAAGTACCTCTTCAAGG                         AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
genomic: GATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
EST: gi|32826105|gb|CD965783.1|CD965783
EST:     GATCTGCAAGTACCTCTTCAAGG                         AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
genomic: GATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
EST: gi|32808552|gb|CD960786.1|CD960786
EST:     AAGTACCTCTTCAAGG                         AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
genomic: AAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
EST: gi|32808172|gb|CD960406.1|CD960406
EST:     GATCTACAAGTACCTCTTCAAGG                         AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
genomic: GATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
EST: gi|15053324|gb|BI358869.1|BI358869
EST:     GCAATGAGATCTGCAAGTACCTCTTCAAGG                         AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
genomic: GCAATGAGATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
EST: gi|32808579|gb|CD960813.1|CD960813
EST:     GATCTGCAAGTACCTCTTCAAGG                         AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA
genomic: GATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGA

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: 30 (upstream exon), 49 (downstream exon)
Score: 849

ATCATCCTCAAGAAGAACAGCAATGAGATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 379

ATCATCCTCAAGAAGAACAGCAATGAGATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 286

ATCATCCTCAAGAAGAACAGCAATGAGATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 430

ATCATCCTCAAGAAGAACAGCAATGAGATCTGCAAGTACCTCTTCAAGGgtatggtcca ... gctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC
                                gtttgat  putative branch site (score: 430)
                                     atgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGTGATCAAGCTCATGCAGAGCTTTAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT