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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacctttgaaatttgaatgcagtactctagtttggctgttgaagcttatatttctgcttgttacttttag

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 5
ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacctttgaaatttgaatgcagtactct-agtttggctgttgaagcttatatttctgcttgttacttttag--------------------------
||||  ||||||||||||||||||| || || || |||||||||||||| ||||||||||||||||| ||||| |||||||   |         | ||  ||  |  || |  |  |||||||||||   ||   |||||   |||||| |||                            
ATGAGGCTCGGGTTAAGGAGTTCAACCTAAAGCAAATGTGGAAGAGCCCCAATGGCACAATTAGGAATATTATCAATGgtatgctggtaccattagtttgatataacacacagaaattggctgttgacatttccctttct---tgttacctttgacatttcgctttcgttttacctttcag
















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|148957374|gb|EC903424.2|EC903424
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211301308|gb|FL411053.1|FL411053
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211348619|gb|FL403648.1|FL403648
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCTTATTATATGCAAAAAACGTTCCAAGACTTGTT
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAA-CGTTCCAAGACTTGTT
EST: gi|211317120|gb|FL381346.1|FL381346
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|6695772|gb|AW288850.1|AW288850
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGGTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211332798|gb|FL423282.1|FL423282
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|149110655|gb|EE190535.2|EE190535
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211245761|gb|FL421854.1|FL421854
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211158137|gb|FL392765.1|FL392765
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTA
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTA
EST: gi|33101480|gb|CF061440.1|CF061440
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|31612230|gb|CD568852.1|CD568852
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|67031198|gb|CO459947.1|CO459947
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211531114|gb|FL426904.1|FL426904
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAWCGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|149031177|gb|EE286335.2|EE286335
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211264490|gb|FL417909.1|FL417909
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211003472|gb|FL408513.1|FL408513
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGC-TATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|29130876|gb|CB381580.1|CB381580
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211097134|gb|FL375411.1|FL375411
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|31356012|gb|CD440369.1|CD440369
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|74237580|gb|DT645494.1|DT645494
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|148937601|gb|EC881791.2|EC881791
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|76286556|gb|DV026124.1|DV026124
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211516468|gb|FL412101.1|FL412101
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211414079|gb|FL428571.1|FL428571
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|32845300|gb|CD984981.1|CD984981
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|60343928|gb|DN210901.1|DN210901
EST:     CAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: CAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211113009|gb|FL402637.1|FL402637
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCC
EST: gi|148961311|gb|EE012038.2|EE012038
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|149055178|gb|EE156095.2|EE156095
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211392274|gb|FL373436.1|FL373436
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|6695773|gb|AW288851.1|AW288851
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAG-CTATTATATGC-AAAACG-TCCAAGACTTG-TC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|50338700|gb|CO533826.1|CO533826
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|32844807|gb|CD984488.1|CD984488
EST:     GAACCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|211214727|gb|FL396531.1|FL396531
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|32844692|gb|CD984373.1|CD984373
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGACCATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAACCGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
EST: gi|18659665|gb|BM500459.1|BM500459
EST:     GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAAC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAAC
EST: gi|32940854|gb|CF045673.1|CF045673
EST:     GAAACACATGTGGAAGAGCCCAAATGACACAATTAGGAACATTATAAATG                         GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC
genomic: GAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTC

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), 49 (downstream exon)
Score: 166

ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 828

ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1043

ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 873

ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacc ... ttacttttagGCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagtacctttgaaatttgaatgcagtactctagtttggctgttgaagcttatatttctgcttgttacttttag

- - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - -  GGAAGA