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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccaaagcacttagttcacgcggagagagaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
gtacccaaagcacttagttcacgcggagagagaactt---ttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
|||| ||      |  ||||||  | |  || ||  |    | | | |     |||||||||  | ||| | || |||| |||||||| |||| ||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||| ||
gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatct-gatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------gtacccaaagcacttagttcacgcggagagagaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
                              |         |  |  |||||  |  |         |||   |    |  | || || || |  || |  |    ||| |||| |||||||| || |||||| |  | || ||||||||||| ||||| || || || |||| ||| ||||| ||||| |||||||| |||||||| |||||
gtataacaagtttatgagcatcttctgatttcattgttatagatttttcacttgctgtatattgccttgtatagtctgtcgctgttactgaaatttatatatgactttgcagTTAGGTCGGCCAAGTTTATTCCGCGCAAGCAATGGGTTGTGGCTGGAGCGGATGATATGTACATCCGTGTATACAATTACAATACAATGGACAAGGTCAA

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacccaaagcacttagttcacgcggagagagaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
|||    |   |     |    |         |   ||| ||        || ||  ||| | | |  ||   || |   ||||  |||| ||||| || ||| || |||| || |||||||||||||| || || |||||||| |||||||||||||||||||| || ||||| ||  ||||
gtatgatatatagcatctcattgttccttcttattctttcgcacatcatttgttg--aatctctgtcctggtgttgt--gcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------gtacccaaa---gcacttagttcacgcggagagagaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
                   |||     |     | ||||     |  ||  |  ||    ||      |  | || ||  |    ||    ||  || ||||  | || |||||||||||| |  | || || ||| | ||||| ||  | ||||||||||||||||| ||||||||||| || || ||||| ||||| ||
gttgcatttttactttcttccagctttgtttccatttcaaagttattgatgaaattcactgaatgaagttcttctcattcactccttccgttt-cttgcagTTCGATCAGCAAAATTTATTCCTCGCAAGCAGTGGATAGTAGCGGGCTCTGACGACATGTTCATTCGAGTCTACAACTATAACACGATGGATAAAGTGAA

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ09529 (Selaginella moellendorffii), 3'ss of exon 2
--------------------------gtaccc--aaagcactt-----agttcacgcggagaga----gaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
                          || ||   | || | ||     |||    |  |    |    ||  |||    | |       |  | | ||| |  | |   |||  ||  |||  | ||||| || || || ||  | || || ||| | || |||||||| |||||||||| |||||| |||||||||||||||||||||||||| |||||
gtaacttttggagtggatttctctaagtccctcgagagtatttttccaagtctgtgttgctccatctcgatttttctaagtttctctctaaaccattgtgtgatct---cttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ36319 (Selaginella moellendorffii), 3'ss of exon 2
--------------------------gtacccaaagcacttagttcacgcggagagagaacttttggcgatc------aggatgatgctaatgtatattttgaact--tattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
                          || ||   ||    |  |||       | |        |  ||||       ||  |    ||||   ||  | ||| ||  |  ||  |||  | ||||| || || || ||  | || || ||| | || |||||||| |||||||||| |||||| |||||||||||||||||||||||||| |||||
gtaacttttggagtaaatttctctaagtcccttgagagtatttttccaagtctgtgttgctccatctcgatttttctaagtttctctctaaaaaattgtgtgatctcttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA

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|18655015|gb|BM499820.1|BM499820
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGGAAACAATGGGTTGTAGCTGGTGCA
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAA-GGAAACAATGGGTTGTAGCTGGTGCA
EST: gi|78122343|gb|DV540727.1|DV540727
EST:     GCAATGGTGAAATCATTTGAAGTTTCAAAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|18654986|gb|BM499791.1|BM499791
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|22489991|gb|BU049914.1|BU049914
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|18655044|gb|BM499849.1|BM499849
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|18655016|gb|BM499821.1|BM499821
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|18662028|gb|BM501705.1|BM501705
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGTAAACAATGGGTTGTAGCTGGTGCA
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGG-AAACAATGGGTTGTAGCTGGTGCA
EST: gi|32930849|gb|CF035661.1|CF035661
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTGGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|89106409|gb|DY576626.1|DY576626
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|18655043|gb|BM499848.1|BM499848
EST:     GCAATGGTTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAAC
genomic: GCAATGGT-GAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAAC
EST: gi|18654807|gb|BM499612.1|BM499612
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGTAAACAATGGGTTGTAGCTGGTGCA
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGG-AAACAATGGGTTGTAGCTGGTGCA
EST: gi|22489999|gb|BU049922.1|BU049922
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|18649626|gb|BM498445.1|BM498445
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|32933566|gb|CF038378.1|CF038378
EST:     GCAATGGTGAAATCGTTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
EST: gi|18661996|gb|BM501688.1|BM501688
EST:     GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG                         TGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG
genomic: GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAG

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), 48 (downstream exon)
Score: 145

GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 79

GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAGgtacccaaag ... ttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
                         tgctaat  putative branch site (score: 110)
                                            cttattttc  putative PPT
                            taatgtatattttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccaaagcacttagttcacgcggagagagaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA