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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacttgcactgttctatctctctgtctattggtttaatggttgcactgctctgcttgtttgttgttgtgcttatcttttattcatcataatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT

Basic information

species Zea mays
transcript GRMZM2G074024_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074024_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g40260.1 (Oryza sativa), 3'ss of exon 1
ttcacttgcactgttctatctctctgtctattggtttaatggttgcactgc-tctgcttgtttg-ttgttgtgcttatcttttattcat--cataatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT-
    ||     ||    || |    ||   || |     |  |    || |  ||||||||||| |||    |||  || | ||| |||  | ||| ||| |||| | |||||| | |||||| ||||| ||  | |||||||||  || ||||| || ||||| ||||||||| ||||||| |||||||||||||| |||||  
----ctaaagatgcatcatatggtagttcgttcgcactgtaatgttgcttcgcctgcttgtttgattgagtggctcttcctgtatgcatgtcctaaacaaacagG-CAATGGATATGGATGATATGCTCGGTGGCCTGCGTGTTGCCGGAGTGCCGACCAAGAGCGCAATTTACTTATGGGGGTATAACCACAGTGGGCAGACGG
















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|211081940|gb|FL387342.1|FL387342
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|76933450|gb|DV173464.1|DV173464
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|91872846|gb|EB402803.1|EB402803
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|211305390|gb|FL411424.1|FL411424
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|211129102|gb|FL371420.1|FL371420
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|211432003|gb|FL420683.1|FL420683
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|29543619|gb|CB603999.1|CB603999
EST:     CCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: CCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|211047338|gb|FL129969.1|FL129969
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|211158187|gb|FL395436.1|FL395436
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|211019672|gb|FL390358.1|FL390358
EST:     GAATCCGCCCAAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|211204474|gb|FL397884.1|FL397884
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|76021288|gb|DT948458.1|DT948458
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|71420798|gb|DR805186.1|DR805186
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
EST: gi|76930470|gb|DV172399.1|DV172399
EST:     GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAG                         GGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC
genomic: GAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCC

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: 45 (upstream exon), 45 (downstream exon)
Score: 38

TTTCCACCGGTCAAACTAGGAGAAGCAAGCAAAGCTCCCCGCCATTAGTAGAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

TTTCCACCGGTCAAACTAGGAGAAGCAAGCAAAGCTCCCCGCCATTAGTAGAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 27

TTTCCACCGGTCAAACTAGGAGAAGCAAGCAAAGCTCCCCGCCATTAGTAGAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 94

TTTCCACCGGTCAAACTAGGAGAAGCAAGCAAAGCTCCCCGCCATTAGTAGAATCCGCCCGAAGTCTGCCCCGCTCTTCGGCCTCGTCCCTTCTCTCCAGgtgagcgctg ... aatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgctctgcttgtttgttgttgtgcttatcttttattcatcataatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT
                           ttatcttttattcatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcacttgcactgttctatctctctgtctattggtttaatggttgcactgctctgcttgtttgttgttgtgcttatcttttattcatcataatcaaccagGGCCATGGATGTAGATGATGTGCTCAGTAACTTGCGTGTTGTTGGTGTGCCAACAAAGAGTGCAATTTACATATGGGGTTATAACCACAGTGGCCAGACT

- - cttgcac
- - - - - - - - - - - - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - - - - - actgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt