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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattcatggggttgactttttattattttaataatattataagtattgttctactaattcgacttttgttaataattaggttacatggtcgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG

Basic information

species Zea mays
transcript GRMZM2G074373_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074373_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g13170.2 (Oryza sativa), 3'ss of exon 3
tgattcatggggttgactttttattatttta-ataatattataagtattgttctactaattcg--acttttgttaataattaggttacatggtcgtttt--gcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG
      ||||     |  |   ||||| | | ||   | |     ||   | | ||  |||    |   | ||   | ||    | ||       ||||  ||||| |||||||||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||||||||||||||||||||
-----aatggataaaaaatgacattatctcagattgcagttctcatagcatgcgacagatttagaaagatagtatgttatgtactcactctcctttttttagcagGGATATCCTCCAATTCCACCACATGGCTTCTTTCCATCACCTGTGGCGTCAAGCCCACAGGGTCATCCTTACATGTGGGGAGCTCAG

upper sequence: GRMZM2G074373_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 3'ss of exon 3
tgattcatggggttgactttttattatttta-ataatattataagtattgttctactaattc--gacttttgttaataattaggttacatggtcgtttt--gcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG
   || ||||     |  |   ||||| | | ||   | |     ||   | | ||  |||    |   | ||   | ||    | ||       ||||  ||||| |||||||||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||||||||||||||||||||
--cttaatggataaaaaatgacattatctcagattgcagttctcatagcatgcgacagatttagaaagatagtatgttatgtactcactctcctttttttagCAGGGATATCCTCCAATTCCACCACATGGCTTCTTTCCATCACCTGTGGCGTCAAGCCCACAGGGTCATCCTTACATGTGGGGAGCTCAG
















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|93013445|gb|EB638965.1|EB638965
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|211035651|gb|FK982762.1|FK982762
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|8367371|gb|BE050316.1|BE050316
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|211035650|gb|FK982761.1|FK982761
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCT
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCT
EST: gi|71318161|gb|DR795843.1|DR795843
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|78090597|gb|DV518971.1|DV518971
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|148976204|gb|EE025907.2|EE025907
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCCTC-CCTGTGGCATC
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCC-TCACCTGTGGCATC
EST: gi|148963993|gb|EE015131.2|EE015131
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|148930175|gb|EC872560.2|EC872560
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|71439024|gb|DR820074.1|DR820074
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
EST: gi|71426949|gb|DR807999.1|DR807999
EST:     CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAG                         GCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCA

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: 190

GAGCAGCAACAACCTGCTACCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

GAGCAGCAACAACCTGCTACCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GAGCAGCAACAACCTGCTACCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 123

GAGCAGCAACAACCTGCTACCTCAGGTGCTGCAACACCGGCTGTTTATCCAGACTGGTCCAGCTTCCAGgtgagtgtga ... cgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttctactaattcgacttttgttaataattaggttacatggtcgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG
                                            tcgtttt  CT-rich tract
                 acttttgttaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattcatggggttgactttttattattttaataatattataagtattgttctactaattcgacttttgttaataattaggttacatggtcgttttgcagGCATATCCTCCAATCCCACCACATGGGTTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTACATGTGGGGAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA