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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcattaccgatatctcttgaacttttatttgctcaccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG

Basic information

species Zea mays
transcript GRMZM2G011893_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g01410.1 (Oryza sativa), 3'ss of exon 5
tggcattaccgatatctcttgaacttttatttgctcaccagtttact--tttggtgcatgat-tatgttgttgt-tgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG
    ||      |   |   || |    | ||| |  |  | || ||  ||    ||||||| ||| | || |  ||||||| | ||  || ||   | ||||| |   ||||||||||||||||||| | ||||| |||||  |||| |||||||||||||||||||||||||||||||| || |||| | | ||  |||| |
----atggtaattgaatacagaccaccaaattgttgccatgctttctagttatacgcatgatgtatttggtggcatgttaatgtacttcatgcttcgtttgcagCGTGAGAGTTTTACCCATAAAATGAGTGATGGGTGGGGGTTGGCTACTGATGGAAAAGTTCTTTTTGGCAGTGATGGTACTTCAAGGTTATACCAGCTTG

upper sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G24430.1 (Glycine max), 3'ss of exon 2
tggcattaccgatatctcttgaacttttatttgctca----ccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaata-tgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG
   |||| | || ||  || | | |  | |  | | |    |||   | | | |    |||   ||    | | |   |||   | ||| |    | |  || ||     ||  ||||  |||   |||  |||||||||||||||||| ||||||||||||||  | ||||| |||||||| |  ||||   ||||| |  | |
-atcattcctgagatg-ctagcagtgatgtggggtgaatgcccaaagtgcctgtta-acatagctagccagatct--ctaacagcttattttgcaatttctgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG

upper sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G24440.1 (Glycine max), 3'ss of exon 5
tggcattaccgatatctcttgaacttttatttgctcaccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG
|    ||   | | | || |     ||| |  | |        |  | |    || |   ||   || | |     |  |  | | |||    | || ||     ||  ||||   || | |||  ||| |||||||||||||| ||||||||||||||  | ||||| ||||||||||  ||||   ||||| |  | |
ttttgtttttgttgtttcatacttctttctgagatgctatcagtgatatgatagcgtagctagcctgatctcaaacagcttatttttacaatttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG

upper sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G24450.1 (Glycine max), 3'ss of exon 5
tggcattaccgatatctcttgaac--ttttatttgc--tcaccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG
     || | || || || | |    | | |  ||   || |||   | | | |    |||    |  | | | |     |  |    | ||     | || ||     ||  ||||  ||| | |||   ||||||||||||||||| ||||||||||||||  | ||||| ||||||||||  ||||   ||||| |  || 
---ttttcctgagatgtcatcagtgatgtgaggtgaaatccccaaagtgcctgtta-acatagccacctagatctcaaacagcttacttttagaatttctgtagATTGGGACATTTAATCATGATATGAATGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATGA

upper sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G29760.2 (Glycine max), 3'ss of exon 5
tggcattaccgatatctcttgaacttttatttgctcaccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG
            | | |  |  ||  |  | |||   |||   | | | |    |||   ||    | | |    |  || || | |||    | || ||     ||  ||||  ||| | |||  |||||||||||||||||| |||||||||| | |  | ||||| ||||||||||  ||||   ||||| |  | |
-----------gtttttgctttaccctcctatgcc--ccaaagtgcctgtta-acatagctagccagatctcaaaagcttact-tttacaatttctgtagATTGGGACATTTAATCATGATATGAAAGATGGTTGGGGTCTGGCAACTGATGGAACATTGTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATTG

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|18964079|gb|BM660797.1|BM660797
EST:     CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAA                         CGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
genomic: CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
EST: gi|19057799|gb|BM736466.1|BM736466
EST:     CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAA                         CGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
genomic: CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
EST: gi|78122303|gb|DV540687.1|DV540687
EST:     CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAA                         TGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
genomic: CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
EST: gi|8383251|gb|BE056194.1|BE056194
EST:     CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAA                         TGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
genomic: CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
EST: gi|71446780|gb|DR827830.1|DR827830
EST:     CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAA                         TGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
genomic: CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
EST: gi|149102642|gb|EE287999.2|EE287999
EST:     CCTGGTTGAAGAACGACGGGTTTATATATGAACGGCATAACTTCTCCCAA                         TGCACCGAGTTTTACC
genomic: CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCAC-GAGTTTTACC
EST: gi|78122304|gb|DV540688.1|DV540688
EST:     CCTGGTTGAAGAACGACGGGTTTATATATGACCGGTATAACTTCTCCAAA                         TGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT
genomic: CCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGAT

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), 47 (downstream exon)
Score: 150

ATTGTTTCAGGTTACCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 153

ATTGTTTCAGGTTACCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 193

ATTGTTTCAGGTTACCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 86

ATTGTTTCAGGTTACCTGGTTGAAGAACGACGGGTTTATATATGACCGGCATAACTTCTCCAAAgtatgctgcc ... gaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttggtgcatgattatgttgttgttgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG
                          tgttaat  putative branch site (score: 86)
                            ttaatttcctatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcattaccgatatctcttgaacttttatttgctcaccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - -ctcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt