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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttccagacatttgactatgtagtctctatgtgatcatctgatatagcatgcatatgttttattgcttatttttatttgattgcctttttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG

Basic information

species Zea mays
transcript GRMZM2G133988_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133988_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 9
tctttccagacatttgactatgtagtctctatgtgatcatctgatatagcatgcatatgttttattgcttatttttatttgatt--gcctttttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG
  |    | |  |   ||    ||  |   |  || | || |  | |  |   |      | | |  ||   || || ||||||   |    |||| | ||||||| |||| |||||||||||||||||||| ||| ||||||||||  ||||||||
aatagttaaat-tgaaaccgcataagcataagctgttgatgtc-tctctctctctctctctctctctctctcttatacttgatttcactacatttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG
















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|211485260|gb|FL406758.1|FL406758
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGNGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211297290|gb|FL430291.1|FL430291
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|13382157|gb|BG458832.1|BG458832
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211084567|gb|FL380768.1|FL380768
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211445219|gb|FL371640.1|FL371640
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211476197|gb|FL374877.1|FL374877
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211199607|gb|FL408270.1|FL408270
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211413964|gb|FL425524.1|FL425524
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211201683|gb|FL384209.1|FL384209
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGNGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|32849674|gb|CD989355.1|CD989355
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCCCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211150179|gb|FL390454.1|FL390454
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|31356659|gb|CD441016.1|CD441016
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|33100114|gb|CF060074.1|CF060074
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211282426|gb|FL393385.1|FL393385
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|211228096|gb|FL409262.1|FL409262
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGC
EST: gi|166431623|gb|EG098503.1|EG098503
EST:     GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG                         ATTTTTTAGCGACTACCGGTTTGATGTATCAAAAC
genomic: GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAAC

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), 44 (downstream exon)
Score: 25

GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 38

GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 32

GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctatag ... ttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcatgcatatgttttattgcttatttttatttgattgcctttttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG
                               atttgat  putative branch site (score: 32)
                          tttttatttgattgcc  CT-rich tract
         atatgttttattgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttccagacatttgactatgtagtctctatgtgatcatctgatatagcatgcatatgttttattgcttatttttatttgattgcctttttttctccagATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG

- - -ccagaca
- - - - - - - - - - - - - - ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - -agcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc