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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctatacatgctgatccaccagccttaccctattagcttgaatttcttctgtttttacgcacggttcctttgattgtattcgatctaccattaccatgcatgaggagatcattattattttgtagataaaaatattctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC

Basic information

species Zea mays
transcript GRMZM5G881387_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G881387_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g48229.1 (Oryza sativa), 3'ss of exon 1
gtatatctatacatgctgatccaccagccttaccctattagcttgaatttcttctgtttttacgcacggttcctttgattgtattcgatctaccattaccatgcat-gaggagatcattattattttgtagataaaaatattctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC
                                      | |||  || ||||| | |  |    |   |      ||    | ||  | |     |||   | ||  | || |||| ||| |  |||||                |||||||| |||||||||||||| ||||||||||| || || | ||| ||||||||||| |||||||| ||||| || ||| |||||||| |||| || ||||||||
--------------------------------------tggctgtaacttcttttctcctgtttcttaggcgtaatgtaactgttaaagcagattttattgttcaaagtggggatctttaattctttgtga--------------tgtgcagACTGCTACTTCACAACAAAGGGATGGAATGCTCAAACCGCTGGAGCTGCAGCTGTTCTTGTTGCCGATGATAGATTGGAGCCTTTGATAACAATGGACTC
















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|149080543|gb|EE169581.2|EE169581
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|148941690|gb|EC886638.2|EC886638
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCT
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCT
EST: gi|148962771|gb|EE013682.2|EE013682
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|148982822|gb|EE028662.2|EE028662
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|149062894|gb|EE157615.2|EE157615
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|148953630|gb|EC898987.2|EC898987
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|149009841|gb|EE041718.2|EE041718
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|211192275|gb|FL063588.1|FL063588
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCA
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCA

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 3 RNA-Seq libraries.


Block sizes: 35 (upstream exon), 24 (downstream exon)
Score: 5

AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC


Block sizes: 25 (upstream exon), 34 (downstream exon)
Score: 3

AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 367

AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatgcatgaggagatcattattattttgtagataaaaatattctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC
                                         tattctct  CT-rich tract
              agatcattattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatctatacatgctgatccaccagccttaccctattagcttgaatttcttctgtttttacgcacggttcctttgattgtattcgatctaccattaccatgcatgaggagatcattattattttgtagataaaaatattctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA