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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtgctatgagactcctttgattccattgtactcagttttatcttaaatctttctgcagatcttacttaggttaacttggtcttagcgcgtatc...

Basic information

species Zea mays
transcript GRMZM2G124886_T04
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 12
CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtgc---------tatgagactcctttgattccattgtactcagttttatcttaaatctttctgcagatcttacttaggtta-acttggtcttagcgcgtatc
 |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| | || ||||||||||||||||| |||||    | |||         ||| | | | ||||| ||   || |||  | | | ||  | ||||||| |||| | ||   |||| |    ||  ||             
TAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctgccctatcccctataatatttctttgttttt-ttctacctattctcatgcttaatcttt-tgcacacctgtattagatcgtgctcagttgctc--------

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 21
CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgt--cttctgtgctatgagactcctttgattccattgtactcagttttatcttaaatctttctgcagatcttacttag-gttaacttggtcttagcgcgtatc-----
 |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| | || ||||||||||||||||| |||||  | |||||    |    | || |  |    |  |||| ||||||         | ||  | | |||  |  |||| | |   |   || || |  | |       
TAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctgtctcttttttccccctccaa---aaggtacccagtttct-----ggtgttaatactgatgatttttagtgatgtttccatcctaacaggcagaatgcc
















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|33093602|gb|CF053596.1|CF053596
EST:     CTAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGT
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGT
EST: gi|32794634|gb|CD946870.1|CD946870
EST:     GATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: GATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|211291669|gb|FL235609.1|FL235609
EST:     CTAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|67014399|gb|CO443148.1|CO443148
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|19822105|gb|BQ048129.1|BQ048129
EST:     CTAGCAAAGTCCCTGAGAATGTAGCGTTGTGGAAATAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|19822050|gb|BQ048074.1|BQ048074
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|26455841|gb|CA827424.1|CA827424
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GGAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|19821970|gb|BQ047979.1|BQ047979
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|5847331|gb|AW000410.1|AW000410
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|111145650|gb|EE257974.1|EE257974
EST:     CTAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCCAAA
genomic: -TAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCC-AAA
EST: gi|19822070|gb|BQ048094.1|BQ048094
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|19822158|gb|BQ048182.1|BQ048182
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|32929286|gb|CF034098.1|CF034098
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTA
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTA
EST: gi|19821973|gb|BQ047982.1|BQ047982
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|26456008|gb|CA827591.1|CA827591
EST:     CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAG                         GTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 212

CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 342

CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 389

CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtg ... tgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAAAGTCCCTGAGATTGTAGCGTTGTGGAAAAAGGATCTCCAGAAGgtcttctgtgctatgagactcctttgattccattgtactcagttttatcttaaatctttctgcagatcttacttaggttaacttggtcttagcgcgtatc

- - - - - - - - - - - - - - - - - - - - - - -  GCAAAG