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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcacttcctggattttgcaatatctattttatgttttatgtggttgacatgttttctttcttttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG

Basic information

species Zea mays
transcript GRMZM2G352129_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G352129_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g42600.2 (Oryza sativa), 3'ss of exon 4
gtaagttcacttcctggattttgcaatatctattttatgttttatgtggttgacatgttttctttcttttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG
||||||| |||||||| || ||| | || ||||| ||| |    ||||| | ||||  || ||||  |      ||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| || || |||||||| || || ||||||||||||
gtaagtttacttcctgaatattggattagctattgtatatcac-tgtggcttacatagttccttttat------acagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAGCCATTGTATGTCGCATTTGCACAACGTAAAGAAGACAGGAAGGCGATGTTGCAG
















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|211179932|gb|FL049123.1|FL049123
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|32850911|gb|CD990592.1|CD990592
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGGGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|211205761|gb|FL339666.1|FL339666
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|13516039|gb|BG518315.1|BG518315
EST:     AGGCTCTGGATTTGNTGCTTTCTTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAA
genomic: AGGCTCTGGATTTGTTGCTTTCT-CAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAA
EST: gi|211113500|gb|FL364716.1|FL364716
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAMTGATCATCTGGAAAACCATTGTATGYTGC
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGAT-ATCTGGAAAACCATTGTATGTTGC
EST: gi|32929766|gb|CF034578.1|CF034578
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|211182327|gb|FL049124.1|FL049124
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATT-TATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|32928646|gb|CF033458.1|CF033458
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|211193131|gb|FL329966.1|FL329966
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|166701766|gb|EG180408.1|EG180408
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGC
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGC
EST: gi|101391361|gb|EB817615.1|EB817615
EST:     GCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: GCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|211157245|gb|FL334278.1|FL334278
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|211461945|gb|FL313813.1|FL313813
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|32848176|gb|CD987857.1|CD987857
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|211437282|gb|FL309165.1|FL309165
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|13490826|gb|BG517590.1|BG517590
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|18963650|gb|BM660554.1|BM660554
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
EST: gi|211179931|gb|FL049122.1|FL049122
EST:     AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCT                         TTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA
genomic: AAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCA

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: 558

GTGATGCGTGATCAAAATGGTCTTAGCAAAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 416

GTGATGCGTGATCAAAATGGTCTTAGCAAAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 454

GTGATGCGTGATCAAAATGGTCTTAGCAAAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 603

GTGATGCGTGATCAAAATGGTCTTAGCAAAGGCTCTGGATTTGTTGCTTTCTCAACTCGTGAGGAAGCATCTCAGGCTgtaagttcac ... ttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatatctattttatgttttatgtggttgacatgttttctttcttttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG
                        ggttgac  putative branch site (score: 603)
                              catgttttctttcttt  CT-rich tract
     tctattttatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcacttcctggattttgcaatatctattttatgttttatgtggttgacatgttttctttcttttcttcacagTTAACTGAAATGAATGGCAAAATGATATCTGGAAAACCATTGTATGTTGCATTTGCGCAGCGCAAAGAAGATAGAAAAGCGATGTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG