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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttaccactaacttattagcagaaatcgtcatctttattgtagtgcaaaaatcttccctgatttttcttttttacttttgctgctacttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG

Basic information

species Zea mays
transcript GRMZM2G053019_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053019_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 10
atgtttaccactaacttattagcagaaatcgt-catctttattgtagtgcaaaaatcttccctgatttttcttttttacttttgctgctact-tattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG
   | |  | ||  |  | | || | | |  | |||  |     || |  | |||||||  |||  ||| |||      |  || || |  | | |  ||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||| ||||||| |||||||||||||||||||||||  ||||||||||||
--ttatgtcccttgcagacttgcggtattattgcatgatgtaactaatatacaaatcttatctggctttccttagactatgctgatgtttttctctaaacagAAACAACATGGGTGGATCTCCTGATCAATGGGATAACCGAATGCTCGATCACTTGAAGAATTTTGACCTTAGCAGTCCAGAAGTCAGGCAGCAGTTTG
















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|13562296|gb|BG550516.1|BG550516
EST:     GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCT                         AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
EST: gi|60339807|gb|DN206780.1|DN206780
EST:     ATGTACCGGCAACAACTACAGGATATGGT                         AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
genomic: ATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
EST: gi|78108044|gb|DV526462.1|DV526462
EST:     GAATCCAATGTACCGGCAACAACTACAGGATATGCT                         AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
genomic: GAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
EST: gi|71440310|gb|DR821360.1|DR821360
EST:     GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCT                         AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
EST: gi|211266715|gb|FL294978.1|FL294978
EST:     GGATGCTGCAGAATCCAATGTACCGGCRACAACTACAGGATATGCT                         AAAGAAGCATGGGTGGATCT
genomic: GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAA-CATGGGTGGATCT
EST: gi|211123549|gb|FL444251.1|FL444251
EST:     GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCT                         AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTCGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
EST: gi|149080111|gb|EE169130.2|EE169130
EST:     AACAACTACAGGATATGCT                         AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA
genomic: AACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCA

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: 46 (upstream exon), 49 (downstream exon)
Score: 167

GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 194

GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 134

GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 196

GGATGCTGCAGAATCCAATGTACCGGCAACAACTACAGGATATGCTgtaagtaata ... ttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaaaaatcttccctgatttttcttttttacttttgctgctacttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG
             ccctgat  putative branch site (score: 196)
                   tttttcttttttactt  CT-rich tract
                tgatttttctttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtttaccactaacttattagcagaaatcgtcatctttattgtagtgcaaaaatcttccctgatttttcttttttacttttgctgctacttattgacagAAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - agcagaa