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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcattatgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

Basic information

species Zea mays
transcript GRMZM2G453794_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 12
gtaagcagccaagcattttgtgtatctatgtactataagt--tcaaattgtcattatgag--attagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
|||||| || ||||||| | || || | | |||| |  ||  | | |||   | |  ||   || ||  || |||  | |||| |    ||| | ||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||| ||||||||||| |||||||| |||||||| ||||||
gtaagctgctaagcattctatgcatgtgt-tactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctc----agGGTCGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGGTATTGGGGTTAAGGGAGAAGAAAGTTGGGAAGCCTGGTGGGATGAAGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 46
gtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcat--tatgagattagatttcaa-acccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
          ||| |||      |||||| ||   | |  |   |  | |||       |||||  || |   || |       | ||||| | || || ||||||||||| ||||||||||||||  | || |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||
--------gtaagtatt------atctatttatcttgaactttgacaggcatgtctcatgattattttccctcacacagtgtttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 48
gtaagcagccaagcatt--ttgtgtatctatgtactataagttcaaattgtcatta-tgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
          ||| |||   | | ||||| |||| | |   |   |  | |||| | | |   |   ||||   | |    |  | ||||| | || || ||||||||||| ||||||||||||||  | || |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||
--------gtaagtattatctatttatctttgtattcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 45
gtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcat-tatgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
|||||  |       || | | |||| ||||    | |||    | |  | | | |   |||  |   |||     |    || | ||  | || ||||| |||| ||| |||||||||||||| |||||  ||||||| |||||||| |||||||  |||||||||||||| |||||||||||||||
gtaagtggtgctatcttatttatatc-atgt----tgagtgttgagtaacgtgtttctcattgaacaacaataaaattatgctttcagAGTCGTGGAGGACTTCAAAGAATGGACAAATTGGCTCTTTTACAGAGGTGGAATTGGTGTGAAAGGAGCTGAAAGCTGGGAAGCATGGTGGGAAGAAGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
gtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcattatgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
          ||| ||  | | | |  || | || |    |  | |||    | |   ||||    |       ||  |||| |||||| ||| ||||| ||  | || |||||||| ||||| |||||  ||||||| ||||| ||||| |||| |||||||||||| ||||||||||| ||||||
--------gtaagtatcatttttcta-attttctctctcatggatttgctcatgttttattaaccatttg--ttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ05083 (Selaginella moellendorffii), 3'ss of exon 45
gtaagcagccaagcattttgtgtatctatgtac-tataagttcaaattgtcattatgagattagatttcaaacccttctccct---cttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
                             |||   | || |  || || ||  |    ||||  ||| ||    ||||  | |    | || | ||| || || |||   |||||||| || ||||| || |||  ||||||  | || || ||||||||||| ||||||||||| |||||||| ||||| 
-----------------------------gtaagcacaactgtaatttttctatggttgatt--attccactgtcttcgtcttaacttcagAACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
gtaagcagccaagcattttgtgtatctatgtac-tataagttcaaattgtcattatgagattagatttcaaacccttctccct---cttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
                             |||   | || |  || || ||  |    ||||  ||| ||    ||||  | |    | |||| ||| || || |||   |||||||| || ||||| || |||  ||||||  | || || ||||||||||| ||||||||||| |||||||| ||||| 
-----------------------------gtaagcacaactgtaatttttctatggttgatt--attccactgtcttcgtcttaacttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG

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|22545826|gb|BU098200.1|BU098200
EST:     TGG-TTTTTGCT-CCTATTTATTTAACCCATCTGGATTTGAATGG-AGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|67031292|gb|CO460041.1|CO460041
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|211408837|gb|FL082347.1|FL082347
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|50322941|gb|CO518067.1|CO518067
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|6578074|gb|AW244211.1|AW244211
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|32834891|gb|CD974569.1|CD974569
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|211408045|gb|FL038492.1|FL038492
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|67040750|gb|CO467005.1|CO467005
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|32934894|gb|CF039706.1|CF039706
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|26558188|gb|CA830423.1|CA830423
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG

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: 449

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 292

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 276

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataagttcaaattgtcattatgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
                                tttcaaacccttctcc  CT-rich tract
                          attagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcattatgagattagatttcaaacccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG