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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagtatatttagtccttaactgtcgctttatgttttgaatctctttgaatctgctgacttctggtgtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA

Basic information

species Zea mays
transcript GRMZM2G169095_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g33330.1 (Oryza sativa), 3'ss of exon 12
gttaagtatatttagtccttaactgtcgctttatgttttga-atctctttgaatctgctgacttct-----ggtgtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA
||| |||| ||||    |  ||||     ||| || |   | || |  | |   ||  |   ||||     ||| | | ||||||| || |||||||| ||||||||||||||||||||||||||||| |||||||| |  ||||||||||||||||||||||| 
gttgagtacatttcagtccaaactaaaattttgtgataaaagatttactagggcctaattctttctatggtggtatgcttgcagTATCTTGATGGTACTACAGACATTACAAGAACTGTACATTTTGGGAAACCCTCTGAGCATGAGAAGTCATGCTACACAGCT

upper sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g45360.1 (Oryza sativa), 3'ss of exon 10
gttaagtatatttagtccttaactgtcgctttatgttttga-atctctttgaatctgctgacttct-----ggtgtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA
||| |||| ||||    |  ||||     ||| || |   | |  |  |||| |||  |   ||||     ||| |   ||||||| || |||||||| ||||||||||||||||||||||||||||| |||||||| |  ||||||||||| ||||||||||| 
gttgagtacatttcagtca-aactcaaattttgtggtaaaagacttgcttgagtctaattctttctatggtggtatgtttgcagTATCTTGATGGTACTACAGACATTACAAGAACTGTACATTTTGGCAAACCCTCTGAGCATGAGAAGTCCTGCTACACAGCT

upper sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g33340.1 (Oryza sativa), 3'ss of exon 11
----------------gttaagtatatttagtccttaactgtcgctttatgttt--tgaatctctttgaatctgctgacttc----tggtgtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA
                ||| | || ||||    |  ||||     ||||||||   |||    || | |   | ||   |      | || | | ||||||| || |||||||| |||||||| |||||||||||||||||||| ||||| || |  ||||| ||||||||||||||||| 
tgacactggggctcaggttgaatacatttcagtccaaactcaaattttatgttagatgacctgctataatcttactctttctatggtagtatgcttgcagTATCTTGATGGTACTACAGACATCACAAGAACTGTACATTTTGGCAAACCATCTGAGCATGAAAAGTCATGCTACACAGCT

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|50323429|gb|CO518555.1|CO518555
EST:     GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAG                         TACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC
genomic: GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC
EST: gi|32833772|gb|CD973450.1|CD973450
EST:     GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAG                         TACCTGGATGGTACAACAGACATTACAAGAACTGT
genomic: GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGT
EST: gi|67018778|gb|CO447527.1|CO447527
EST:     GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAG                         TACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC
genomic: GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC
EST: gi|211089691|gb|FL030410.1|FL030410
EST:     GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAG                         TACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC
genomic: GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC
EST: gi|32834344|gb|CD974022.1|CD974022
EST:     GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAG                         TACCTGGATGGTACAACAGACATTACAAGAACTGT
genomic: GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGT
EST: gi|32937410|gb|CF042229.1|CF042229
EST:     GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAG                         TACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC
genomic: GTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCC

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: 47 (upstream exon), 49 (downstream exon)
Score: 218

TGTGGGACCAAATGCAGCAGTTATTCACTATAAACCTGAAGCAAGCACATGTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA


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

TGTGGGACCAAATGCAGCAGTTATTCACTATAAACCTGAAGCAAGCACATGTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 237

TGTGGGACCAAATGCAGCAGTTATTCACTATAAACCTGAAGCAAGCACATGTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

TGTGGGACCAAATGCAGCAGTTATTCACTATAAACCTGAAGCAAGCACATGTTCGGAAATGGATGCTGATAAAATATATCTTTGTGACTCTGGGGCACAGgttaagtata ... gtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcgctttatgttttgaatctctttgaatctgctgacttctggtgtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA
                               tgctgac  putative branch site (score: 274)
      tttatgttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagtatatttagtccttaactgtcgctttatgttttgaatctctttgaatctgctgacttctggtgtacatgcagTACCTGGATGGTACAACAGACATTACAAGAACTGTACATTTTGGTAAACCCTCAGCACATGAGAAGTCATGCTACACAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT