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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcattagcactgatcaagactgtatgaacgagtaaacatcctttgggacaacttggtcatttttttctcacgaagttgtccccttttatcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG

Basic information

species Zea mays
transcript GRMZM2G171406_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g43594.3 (Oryza sativa), 3'ss of exon 7
gtgcattagcactgatcaagactgtatgaacgagtaaacatcctt-tgggacaacttg--gtcatttttttctcacgaagttgtccccttttatcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG-------------------------
 |  |  |    | |  ||   ||  ||||| |  ||||||| || ||  |     ||   || ||||||||| |   ||    | | |||| |  || |||||| |||||||| || || |||||||| |||||||| |||||||| ||||||||||||||||||||||||||||||                         
-tatac-aattttaactaaatttgcctgaacaaagaaacatctttgtgatatgttctgttatcgtttttttcttaattagc-acctcattttcttctattcagATACAGACAATACAACGCTTGAAAGATGAAAGAGATAACATGCTGCAGCAAAATCAGCAAATGCAACGTGAATTGGTCAGCCTTATTTTTTTGCAATTCA

upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 7
gtgcattagcactgatcaagactgtatgaacgagtaaacatcctttgggaca-acttggtcat-----ttttttctcacgaagttgtccccttttatcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG
       |    | | ||||  ||| ||| | |  ||||||| |||| || |   |  || ||     || ||||| ||  ||||  |   |||| |  ||  ||||| |||||||| || ||  | ||||| ||| |||||| ||  || ||||||||||||||||||||||||||||||
-----acaattttaaccaagcttgtctgagcaaagaaacatcttttgtgatatgttctgttatcctttttgtttcttacttagtt-ccttgttttcttctatccagATACAGACAATACAACGCCTAAAAGACGAACGAGACACCACCCTGCAGCAAAATCAGCAAATGCAACGTGAATTG
















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|94475041|gb|EB703999.1|EB703999
EST:     ATGCTGAAGAATGCAAGCCTTGAAGAG                         ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
genomic: ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
EST: gi|16919153|gb|BM074062.1|BM074062
EST:     ATGCTGAAGAATGCAAGCCTTGAAGAG                         ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
genomic: ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
EST: gi|60397188|gb|DN230004.1|DN230004
EST:     ATGCTGAAGAATGCAAGCCTTGAAGAG                         ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
genomic: ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
EST: gi|94475040|gb|EB703998.1|EB703998
EST:     ATGCTGAAGAATGCAAGCCTTGAAGAG                         ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
genomic: ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
EST: gi|78024373|gb|DV492760.1|DV492760
EST:     GAAGAATGCAAGCCTTGAAGAG                         ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
genomic: GAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
EST: gi|5069938|gb|AI737903.1|AI737903
EST:     ATGCTGAAGAATGCAAGCCTTGAAGAG                         ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
genomic: ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
EST: gi|5069940|gb|AI737905.1|AI737905
EST:     CTGATGATGCTGAAGAATGCAAGCCTTGAAGAG                         ATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA
genomic: CTGATGATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAA

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: 37 (upstream exon), 22 (downstream exon)
Score: 4

ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG


Block sizes: 44 (upstream exon), 36 (downstream exon)
Score: 3

ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG


Block sizes: 9 (upstream exon), 41 (downstream exon)
Score: 1

ATGCTGAAGAATGCAAGCCTTGAAGAGgtaatacgct ... tcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggacaacttggtcatttttttctcacgaagttgtccccttttatcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG
                                ttgtccccttttatct  CT-rich tract
             tcattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcattagcactgatcaagactgtatgaacgagtaaacatcctttgggacaacttggtcatttttttctcacgaagttgtccccttttatcttactcagATCCAGACAATTCAGCGGTTGAAAGAAGAAAGAGACAACATGCTTCAGCAAAATCAGCAAATGCAACGTGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA