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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtccggcatcttgtgtttctgttgtaaatttgaccttgtattcgtgtctaacctttttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG

Basic information

species Zea mays
transcript GRMZM2G450055_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 14
gtatgtccggcatcttgtgtttctgt----------tgtaaatttgaccttgtattc-----------gtgtctaacctttttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG
|| ||   ||| |  | ||||    |             |  |||||  |  | |||            ||  ||| | |   |||| |||||||||| |||| |||||||  || || |||||||| || |||||||| ||||| |||||||| |||||||||||| | ||||||||||||
gtgtggttggccttctatgttctgatatacatactacacagttttgatatgatgttcttggattgtaaatgcataatcctcacatgtgtagGTACATTGAGTATTGCCGTGTTACTTGTAAACCACGACTCTCAGAAAAGGCAGCAGAGATGCTTCAGAACAAATATGTGGAGATTAGACAG
















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|18385259|gb|BM418458.1|BM418458
EST:     GCGTCATCGGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|19822727|gb|BQ048751.1|BQ048751
EST:     CATCGGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCG-GCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: CATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|87152446|gb|DY397235.1|DY397235
EST:     GCGTCATCGGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|17970225|gb|BM276989.1|BM276989
EST:     GCGTCATCGGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|19821812|gb|BQ047836.1|BQ047836
EST:     AGAGAA-TGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGTTTTTCAGAAAAAG
genomic: AGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGG-CTTTCAGAAAAAG
EST: gi|22490113|gb|BU050036.1|BU050036
EST:     GCGTCATCGGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|22473134|gb|BU037614.1|BU037614
EST:     GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAA-G                         GTACATTCAGTACT
genomic: GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACT
EST: gi|17970308|gb|BM277071.1|BM277071
EST:     TGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: TGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|19822728|gb|BQ048752.1|BQ048752
EST:     GCGTCATCGGCAAACNCAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGC
genomic: GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGC
EST: gi|18450531|gb|BM428809.1|BM428809
EST:     GCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: GCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|22545894|gb|BU098253.1|BU098253
EST:     GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
genomic: GCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC
EST: gi|18385107|gb|BM418306.1|BM418306
EST:     GAATTGGCTTAAAAG                         GTACATTCAGTACTGCCGTGCAACATGCAAACCACGTCTTTCAGAAAAAGC
genomic: GAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 76

CGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCAGCAGCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 16

CGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCAGCAGCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 29

CGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCAGCAGCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG


Block sizes: 36 (upstream exon), 44 (downstream exon)
Score: 5

CGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCAGCAGCGTCATCCGCAAACACAGAGGGAAGTGAAGGAGAGAATTGGCTTAAAAGgtatgtccgg ... ttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttctgttgtaaatttgaccttgtattcgtgtctaacctttttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG
                                  gtctaac  putative branch site (score: 5)
                                        cctttttat  CT-rich tract
                                          tttttatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtccggcatcttgtgtttctgttgtaaatttgaccttgtattcgtgtctaacctttttatgtatagGTACATTCAGTACTGCCGTGCAACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG