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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggttcaacatgccttgaaaatttagatgtgctgttctatgagtttttggcattatagtcattattgctcgattgatgcatgtgtcacttcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG

Basic information

species Zea mays
transcript GRMZM5G813909_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 11
-------ttggttcaacatgccttgaaaatttagatgtgctgttctatgagtttttggcattatagtcattattgctcgattgatgcatgtgtcacttcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG
       |  |||     || |||| |  ||| | ||   |  ||||  | |  |    |||| |    |||   || ||||||    |  ||  ||| ||||| ||||||| ||||||||  |||| ||||||||||| ||||| ||||||||||||||  | |||||||||||||||
tttcatttaagtttgcagtggcttgcattttttggtggatt--tctagtattgctc--tattacaa--gttacaacttgattgacatgtccgttgctt-gattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG

upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 10
----ttggttcaacatgccttgaaaatttagatgtgctgttctatg--agtttttggcattatagtcattattgctcgattgatgcatgtgtcacttcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG-
       |||  |    || ||  | | |   | |   |||| |||  || ||||  |   | ||   |||       ||   | ||  ||    ||   |||||||| ||  |||| ||  | || ||  |  | |||||| | ||||||||||||||| || |||||||||||||| 
atccaaagtttgagcctccatgccattattcttttatagttccatggaagattttatctacaaagcacttaa-----aatcctttcacctg--gatttatttgcagcATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTTGTCAGCCGATCATTTGAATTTCAGG
















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|32909801|gb|CF014613.1|CF014613
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|18165861|gb|BM335700.1|BM335700
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|76293280|gb|DV032848.1|DV032848
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|32914225|gb|CF019037.1|CF019037
EST:     GTTCTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGTTTTTACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|32914224|gb|CF019036.1|CF019036
EST:     GTTCTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|71761327|gb|DR959264.1|DR959264
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|32806461|gb|CD958695.1|CD958695
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|32909800|gb|CF014612.1|CF014612
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|32791671|gb|CD943907.1|CD943907
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|7162447|gb|AW520069.1|AW520069
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTT
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTT
EST: gi|32806368|gb|CD958602.1|CD958602
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|71767567|gb|DR965504.1|DR965504
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|78114997|gb|DV533385.1|DV533385
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|71758092|gb|DR956029.1|DR956029
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|6095666|gb|AW120333.1|AW120333
EST:     GTTTTGGCTTCAAGGNCCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACCCCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
EST: gi|50322420|gb|CO517546.1|CO517546
EST:     GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAG                         CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC
genomic: GTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTC

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: 80

TCAATTTGGAGGATATACTCTAGTAAGGAGCTCCAAAGATCTATTTGGAAGTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 78

TCAATTTGGAGGATATACTCTAGTAAGGAGCTCCAAAGATCTATTTGGAAGTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

TCAATTTGGAGGATATACTCTAGTAAGGAGCTCCAAAGATCTATTTGGAAGTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

TCAATTTGGAGGATATACTCTAGTAAGGAGCTCCAAAGATCTATTTGGAAGTTTTGGCTTCAAGGACCAGCCAGTAATAATTGGATTGATCATTTTCCAGgtatgtttga ... tcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggcattatagtcattattgctcgattgatgcatgtgtcacttcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG
                          gattgat  putative branch site (score: 73)
                                        tcacttc  putative PPT
       attatagtcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggttcaacatgccttgaaaatttagatgtgctgttctatgagtttttggcattatagtcattattgctcgattgatgcatgtgtcacttcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - acatgcc
- - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tattgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt