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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttcccatctcaccatagactttacttgtctttgatttgaaacaaacagattttaaggttgacgatttttttgtgtgtgctcag

Basic information

species Zea mays
transcript GRMZM2G012319_T01
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 24
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 5'ss of exon 22
CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttcccatctcaccat--agactttacttgtctttgatttgaaacaaacagattttaaggttgacgatttttttgtgtgtgctcag
 |||||||||   |||||||||| ||||| || ||||| ||||||||||||||||| ||||||||||| | ||||||  |  ||  |||  |  |||||  |      |||| | |||||||  |||   ||| ||   ||| |  ||||
TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTATgtaagttctcttctcactttctagtttttcttgttctttagtcatgcgcaaaaacattttaatattggttattattgc-tgtatcttcag

upper sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 24
lower sequence: GLYMA08G03020.1 (Glycine max), 5'ss of exon 25
CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttcccatctcaccatagacttta--cttgtctttgat-----ttgaaacaaacagatttta---aggttgacgatttttttgtgtgtgctcag------------------------------------
 ||||||||| | | ||||||||||| || ||||| ||||| || ||||| |||| ||||||||||  |         ||  | |||   |||||||    |     || | | ||  ||| |||     | ||    || |||||     | |  ||                                    
TTGAGTTTAACCGCAGGAGAAGAAGTCGACATTGAGTACGAAGTAGATGGCTGGTTTTATgtaagtctctgatgagatatctatttttatcttgtctgaagtagagatttagataactagaatttgcatggattccttatgtttttaatcatacataggagaatcagttgttgatagcatactttgccatgcag

upper sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 24
lower sequence: GLYMA05G36530.1 (Glycine max), 5'ss of exon 25
CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc-atctcaccatagactttacttgtctttgatttgaaac--aaacagatttta---aggttgacgat-ttttttgtgtgtgctcag------------------------------------
 ||||||||| | | ||||||||||| |||||||| ||||| || ||||| |||| ||||||||||     ||   |  | |   | ||  |    |  | | || |   ||  ||| ||||    | ||    || ||||||     | |  ||                                    
TTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGCTGGTTTTATgtaagtctttgatgagataacaatttgtatcttgtctgaagtagagatttaactagaatttacatggattccttatattttttaatcatacataggagaatcagttgttgatcgcatactttgccgtgcag

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|60352427|gb|DN219400.1|DN219400
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|211048296|gb|FL052136.1|FL052136
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGA
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGA
EST: gi|18661340|gb|BM501362.1|BM501362
EST:     GTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: GTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|60356301|gb|DN223274.1|DN223274
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|22546271|gb|BU098582.1|BU098582
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|26558707|gb|CA830942.1|CA830942
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|211175970|gb|FL481230.1|FL481230
EST:     GTTGGTATTAT                         GTGAAGAAAAGGAGSCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: GTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|91049126|gb|EB159544.1|EB159544
EST:     GAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: GAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|76909470|gb|DV163396.1|DV163396
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|87156397|gb|DY401186.1|DY401186
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|60337974|gb|DN204947.1|DN204947
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
EST: gi|60398288|gb|DN231104.1|DN231104
EST:     ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT                         GTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT
genomic: ACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCT

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), 47 (downstream exon)
Score: 196

CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCTGTTCTGTATGTGAGTTCATGATAACAGCCGTGTGTATCGTTTCCCACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCTGTTCTGTATGTGAGTTCATGATAACAGCCGTGTGTATCGTTTCCCACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 349

CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCTGTTCTGTATGTGAGTTCATGATAACAGCCGTGTGTATCGTTTCCCACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttccc ... gtgtgctcagGTGAAGAAAAGGAGGCCTGGAAGGGATGGAAAGATGGCAGGTCTGGTTCCTGTTCTGTATGTGAGTTCATGATAACAGCCGTGTGTATCGTTTCCCACAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTATgtaagttcccatctcaccatagactttacttgtctttgatttgaaacaaacagattttaaggttgacgatttttttgtgtgtgctcag

- - - - - - - TGGAGA
- - - - - - -  GGAGAA
- - - - - - - - -  AAGAAG
- - - - - - - - - - AGAAGT
- - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - GTGGAG
- - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - GGAGAT