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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaacgaaatgtgaaactactctgcattttgatgtgcaataatgttttccctctaaactgaaatgcttgtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 3'ss of exon 6
gtatttaacgaaatgtgaaactactctgcattttgatgtgcaataatgttttccctctaaactgaaatgcttgtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT
||||||||    || |||| ||| |||  |||   |||   ||  | |||   |    | | ||||    |  ||||||||||||||||||||||||| ||||||||||||||||| || |||||||| |||||||| || ||||||||||||||||||||||| ||||| ||||| |||||
gtatttaagaggatatgaatctattctttattg-aatg---aactaagttcatctgtaacattgaaccattgatgaaaccagGATGGACTAAGCCCATTTGCATTGGAAGGCATGCTTTTGGTGATCAGTACCGAGCAACTGATGCAGTTCTGAAGGGGCCTGGCAAGCTCAAGCTGGTTTT
















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:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|211301308|gb|FL411053.1|FL411053
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTG
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTG
EST: gi|211317120|gb|FL381346.1|FL381346
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|6695772|gb|AW288850.1|AW288850
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGGTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|211332798|gb|FL423282.1|FL423282
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|149110655|gb|EE190535.2|EE190535
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATCCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|33101480|gb|CF061440.1|CF061440
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|31612230|gb|CD568852.1|CD568852
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|67031198|gb|CO459947.1|CO459947
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|211531114|gb|FL426904.1|FL426904
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAWCGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATT
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATT
EST: gi|149031177|gb|EE286335.2|EE286335
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|211264490|gb|FL417909.1|FL417909
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|29130876|gb|CB381580.1|CB381580
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGT
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGT
EST: gi|211097134|gb|FL375411.1|FL375411
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|31356012|gb|CD440369.1|CD440369
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|74237580|gb|DT645494.1|DT645494
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|148937601|gb|EC881791.2|EC881791
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|76286556|gb|DV026124.1|DV026124
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|211516468|gb|FL412101.1|FL412101
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTG
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTG
EST: gi|211414079|gb|FL428571.1|FL428571
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTACGCCCATCTGCATTGTGA-GGCATGCCTTCGGTGATCAATAC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTG-GAAGGCATGCCTTCGGTGATCAATAC
EST: gi|32845300|gb|CD984981.1|CD984981
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|60343928|gb|DN210901.1|DN210901
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|67023195|gb|CO451944.1|CO451944
EST:     TGTGTTTATAGAGCCTATTATATGC-AAAACGTGGCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|148961311|gb|EE012038.2|EE012038
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|149055178|gb|EE156095.2|EE156095
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|211392274|gb|FL373436.1|FL373436
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|6695773|gb|AW288851.1|AW288851
EST:     TGTGTTCAGAGAG-CTATTATATGC-AAAACG-TCCAAGACTTG-TCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|13198145|gb|BG354175.1|BG354175
EST:     AGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: AGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|50338700|gb|CO533826.1|CO533826
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCT
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCT
EST: gi|32844807|gb|CD984488.1|CD984488
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|211214727|gb|FL396531.1|FL396531
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGC
EST: gi|32844692|gb|CD984373.1|CD984373
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAACCGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
EST: gi|32940854|gb|CF045673.1|CF045673
EST:     TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAG                         GATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC
genomic: TGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACC

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: 138

GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 519

GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 495

GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 634

GCACTGTGTTCAGAGAGCCTATTATATGCAAAAACGTTCCAAGACTTGTTCCAGgtatttaacg ... gtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttgatgtgcaataatgttttccctctaaactgaaatgcttgtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT
                           ctctaaa  putative branch site (score: 634)
              aataatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaacgaaatgtgaaactactctgcattttgatgtgcaataatgttttccctctaaactgaaatgcttgtgaaaccagGATGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC