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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatcatgcagcaaaccagtacgagagctgagtccttttgtttttgaaccaacaagagatgagatgagcctcgtttgcctgttccgtgtatatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG

Basic information

species Zea mays
transcript GRMZM2G044382_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------acatcatgcagcaaaccagtacgagagctgagtcctt--ttgtttttgaaccaacaagagatgagatgagcctcgtttgcctgttccgtgtatatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG
                                                                              ||    |  ||      |  || ||   | | |   |  ||| |||  | ||  ||| |   ||||||||     |||| ||  ||      | | ||||||| ||||| || || |||||||||||| ||| |||||| ||||| | |||||| || |||||||| ||||| ||||| || || |||||||||||||||||
gtataataattcctcctgggactaactggctcctagttcttctcacttagtattatcagtagtacagtttactacttaaccctgtctagtctcttatgaccagccgttactgggtgattgctttctaccccgcaataa--gagatgagtacaatttgtctactc-----gtgtgtttcagCCCATTCTTCAGGAACAACCGTGACGTTTGTCATAATCGATGGGTACGTTGTGACCGTTGCATCCGTTGGCGATTCGCGGTGCGTCCTTGAAGCTGAGGG

upper sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 2
--acatcatgcagcaaaccagtacgagagctgagtccttttgtttttgaaccaacaagagatgagatgagcctcgtttgcctg---ttccgtgtatatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG
  |||| ||| || | | || |     |   ||      | || |   |||  ||  | |||  |||     |  |    |||   |    | | | | || |||  ||    || || ||||| || ||  ||| ||| || || || |  |||||||| |||||||| ||||||||||| ||||| ||||||||| ||   | 
aaacatgatgaagaatatcaat-tactaatggaagttaatggtgt---aactgacttgtgatt-gatagtttttatacttctgaattaatatttttttgttacagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTCCTTGAATCTTCTGA

upper sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 3
acatcatgcagcaaaccagtacgagagctgagtccttttgtttttga-accaacaagagatgagatg-agcctcgtttgcctgttccgtgtatatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG
  ||||   |  ||   |     |  |   |      ||||  |||| |      | |  |  |||  |   |  |||   | ||   | |   | || |||  ||    || || ||||| || ||  ||| ||| || || || |  |||||||| |||||||| ||||||||||| ||||| || |||||| ||   | 
--atcaattactaatggaagttaatggtgtaactgacttgtgattgacagtttttatacttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA

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|149071130|gb|EE159529.2|EE159529
EST:     GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAG                         CTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
genomic: GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
EST: gi|148971590|gb|EE022306.2|EE022306
EST:     GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAG                         CTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
genomic: GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
EST: gi|148993132|gb|EE033731.2|EE033731
EST:     GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAG                         CTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
genomic: GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
EST: gi|148939724|gb|EC884406.2|EC884406
EST:     GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAG                         CTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
genomic: GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
EST: gi|88747035|gb|DY531176.1|DY531176
EST:     GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAG                         CTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
genomic: GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
EST: gi|89249221|gb|DY621007.1|DY621007
EST:     GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAG                         CTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG
genomic: GGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTG

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), 49 (downstream exon)
Score: 155

TGCGTCCCGACCGATCTGGCCTGGGACGACTGGCTCGCCGCGCTGCCGAGGGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 59

TGCGTCCCGACCGATCTGGCCTGGGACGACTGGCTCGCCGCGCTGCCGAGGGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 61

TGCGTCCCGACCGATCTGGCCTGGGACGACTGGCTCGCCGCGCTGCCGAGGGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 43

TGCGTCCCGACCGATCTGGCCTGGGACGACTGGCTCGCCGCGCTGCCGAGGGCCCTCGTCGCGGGGTTCGTCAAGACCGACAAGGATTTCCAGACTAAAGgtaactgaaa ... tatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaccaacaagagatgagatgagcctcgtttgcctgttccgtgtatatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG
                                         tgtatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatcatgcagcaaaccagtacgagagctgagtccttttgtttttgaaccaacaagagatgagatgagcctcgtttgcctgttccgtgtatatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- -tcatgca
- - - - - -caaacca
- - - - - - - - - - - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - -caacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttcc