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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctgactgaatttttcatccatccgtcgcctaatttgttgctatttttgctacttattgttaggttcatgtgattttggtatggttagatactt...

Basic information

species Zea mays
transcript GRMZM2G169095_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g33330.1 (Oryza sativa), 5'ss of exon 2
AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctgactgaatttttcatccatccgtcgcctaatttgttgctatttttgctacttattgttaggttcatgtgattttggtatggttagatactt---------------------------------------------------------------------------
||||||||||||||||||| ||| || |||||| ||||| ||||||||||||| |||||||| |||  ||      ||  |  ||| || |||| |  |     ||||| |          | |   |     | ||   ||||| |  || | | | |||  |                                                                           
AGCGAGTACGTGTCGGAGCGGGACAAGCGGCGGCAGTTCGTCTCCGGGTTCACCGGGAGCGCCGgtatgt-----ttgcttccttcctcaatccattccgcctcttgtttcccagccgatgagtccgttgcgagctcgcatgattgtccta-gctcacataaattgccttagaacagtactgggtttcacgagatttggttaggttattgtttgggcatatgcatcgcaatgggtacag

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g45360.1 (Oryza sativa), 5'ss of exon 2
AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgt-gctgactgaatttttcatccatccgtcgcctaatttgttgctatttt-tgctacttattgttaggttcatgtgattttggtatggttagatactt
|||||||| |||||||||| ||| || |||||| ||||| ||||||| ||||| ||||||||||||  || |||  || ||||  ||  |    |||  || |     |      | | |  |          |    |   ||| | || |  | | || |  | 
AGCGAGTATGTGTCGGAGCGGGACAAGCGGCGGCAGTTCGTCTCCGGCTTCACCGGGAGCGCTGgtatgttgcttcctcaattcatc-ccttctcgtttcccaggcgatgaacgctgtgtattgtcctagaccaccagccgatgagtctgttgcgatgagttcat-

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g33340.1 (Oryza sativa), 5'ss of exon 2
AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGA---------GCGCTGgtccgt-gctgactgaatttttcatccatccgtcgccta--atttgttgctatttttgctacttattgttaggttcatgtgattttggtatggttagatactt
|||||||| ||| |||||| ||| || |||| | ||||||||||||||||||| ||||         ||||||||  || |||  || ||  |   ||||||||||| | ||  | ||||       ||   | ||  ||     |   ||| | ||  | |  | | || |    
AGCGAGTATGTGGCGGAGCGGGACAAGCGGCTGCAGTTCATCTCCGGGTTCACCGGGATCGCCCGCAGCGCTGgtatgttgcttcctcaacctca-atccatccgtcccttatgacttgtgagctcattctgtgctagttcaccagccgatgag-ttgggctgcgatgagttcag-

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|20299991|gb|BQ162934.1|BQ162934
EST:     GGAGCAGGATAACCGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|211311977|gb|FK981217.1|FK981217
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|211311973|gb|FK981213.1|FK981213
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|32838356|gb|CD978034.1|CD978034
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|148948656|gb|EC898570.2|EC898570
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATTGAAAAAGGCATTGTTGTGGACGGATGGCCGC
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCAT-GAAAGAGGCATTGTTGTGGACGGATGGCCGC
EST: gi|22489137|gb|BU049060.1|BU049060
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|21987275|gb|BQ778803.1|BQ778803
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGTCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|32838378|gb|CD978056.1|CD978056
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|87298752|gb|DY470755.1|DY470755
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|32939599|gb|CF044418.1|CF044418
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|211311976|gb|FK981216.1|FK981216
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|211311972|gb|FK981212.1|FK981212
EST:     GAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGG-AGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|78113783|gb|DV532172.1|DV532172
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|211311975|gb|FK981215.1|FK981215
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|149085325|gb|EE174831.2|EE174831
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
EST: gi|211311974|gb|FK981214.1|FK981214
EST:     GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTG                         GCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT
genomic: GGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCT

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: 308

AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCTACTTCTTGCAGGCAACACAGCAACTGAGCGATCGTTGGAAACTTATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCTACTTCTTGCAGGCAACACAGCAACTGAGCGATCGTTGGAAACTTATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCTACTTCTTGCAGGCAACACAGCAACTGAGCGATCGTTGGAAACTTATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 449

AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctg ... ttttaaacagGCTTGGCTCTTATCACCATGAAAGAGGCATTGTTGTGGACGGATGGCCGCTACTTCTTGCAGGCAACACAGCAACTGAGCGATCGTTGGAAACTTATGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGAGTACGTGTCGGAGCAGGATAAACGGCGGGAGTTCATCTCCGGGTTCACAGGGAGCGCTGgtccgtgctgactgaatttttcatccatccgtcgcctaatttgttgctatttttgctacttattgttaggttcatgtgattttggtatggttagatactt

- - - - - - - GGAGCA
- - - - - - -  GAGCAG