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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttattacgaatttgaatatcacataccattagcactggcggtcagtcaccatgctatagtgcaggcctcttatttttttgcttgtgaagatcctc...

Basic information

species Zea mays
transcript GRMZM2G168412_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168412_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g74190.1 (Oryza sativa), 5'ss of exon 7
TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttattacgaatttgaatatcacat-accattagcactggcggtcagtcaccatgctatagt---gcaggcctcttatttttttgcttgtgaagatcctc
|||||||||||||||||||||| ||||| || ||||| |||||||| |  || ||||||| | ||||||||||||||||||||||||| || |||||||||||        |       || |  | |  |  |  |  |  |     | |||  ||  | |   |     |    ||| ||||| || ||  | |  |     
TAAAAATTGGGCAAAGGATGATAACAATCTCCACAGTAGGTGTTCCCAGCACTATAAAAAAGTTAGCATCTCACAAGCTTCAGTCAACACTTGCAGTCAGgtacaccccccccccccaaaaaaaaaaaagaaaaagaaaaaagaacacctgtcttcacaccaagatttaataatgttctcattttgttcctccttacaaa----

upper sequence: GRMZM2G168412_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G39670.1 (Arabidopsis thaliana), 5'ss of exon 7
TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttattacgaatttgaatatcacataccattagcactggcggtcagtcaccatgctata-gtgcaggcctcttatttttttgcttgtgaagatcctc-
|  |||| || ||| | ||||| |||||||| || || ||||||||||| ||||| || | ||| |||||||| ||||||||||| ||  | || |||||||  || || ||   ||   || | |   |    | |  |      | |       |  ||||         |||   |  |||| |||          || 
TTGAAATCGGACAACGAATGATTACAATATCGACTGTAGGTGTTCCAAACACAATCAAGAAGCTTGCATCTCATAAGCTTCAGTCGACCTTAGCTGTCAGgtgcgtcatcact--ttctgattttattcatgtgttgttcaattacttaaatgatcttttatacaaatttctctcgagtacttttactttactcagctttct
















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|91878765|gb|EB408722.1|EB408722
EST:     ACAATAAAAATGCTAGCATTTCACAAGCTTCAGTCAACGGGGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|71766718|gb|DR964655.1|DR964655
EST:     AAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: AAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|32803194|gb|CD955430.1|CD955430
EST:     ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|88747606|gb|DY531747.1|DY531747
EST:     ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|13149611|gb|BG319933.1|BG319933
EST:     KCAATAAAAATGCTKGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATSCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|78122643|gb|DV541027.1|DV541027
EST:     ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|60345957|gb|DN212930.1|DN212930
EST:     CTAGCATCTCACAAGTTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: CTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|71328602|gb|DR800966.1|DR800966
EST:     ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|78118843|gb|DV537227.1|DV537227
EST:     ACAATAAAAATGATAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|76286139|gb|DV025707.1|DV025707
EST:     ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
EST: gi|76015835|gb|DT943005.1|DT943005
EST:     ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAG                         TCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA
genomic: ACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAA

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: 47 (upstream exon), 42 (downstream exon)
Score: 54

TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAAGTCTTACCCCTTGGGAGCACTAATGGATGACTGCAAGAGTTACTTCCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 139

TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAAGTCTTACCCCTTGGGAGCACTAATGGATGACTGCAAGAGTTACTTCCTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 35

TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAAGTCTTACCCCTTGGGAGCACTAATGGATGACTGCAAGAGTTACTTCCTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttatt ... ttgaaatcagTCTGCATGCCCCAAATCAGAAGCTGCGGGAGACGATTGTTCCTAGCGCCAAGTCTTACCCCTTGGGAGCACTAATGGATGACTGCAAGAGTTACTTCCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAGTCAGgtatgttattacgaatttgaatatcacataccattagcactggcggtcagtcaccatgctatagtgcaggcctcttatttttttgcttgtgaagatcctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT