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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcattgtccacccctcctatcagtttaagcttttgggttggactgattgatgcatgcaacttaatactcacatttttcttctttgttccacttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG

Basic information

species Zea mays
transcript GRMZM2G136803_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136803_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 16
--tgcattgtccacccctcctatcagtttaagcttttgggttggactgattgatgcatgcaacttaatactcacatttttcttctttgttccacttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG
  | |||| || |   |  |||   |       |  ||  ||   |   |  ||     |  || | | | |      ||  |  || || ||| ||||||||| ||||| || ||||| |||||||||||||| |||| |||| |||| |  ||| ||||||| ||| | ||| | |||||||| ||||  || || ||||
tctccatt-tcaaaatcagctacgtgcactccttactgcatttttccattacatttcgtcctctaatttcccttgcaatttattgtt-ttgcacgtgtatagTTCAAAGAGGACTGCAATACAGAGAAAAAGATAATTGCAAAGCTTAAGAACAGTTCTGAAAAATCATTATGGCTGGAGAAAGAAGACAGCATTCGGCGTG
















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|211541853|gb|FL147715.1|FL147715
EST:     CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG                         TTTAAAGAAGACTGCAACACAGAGAAAAAGATTATTATAAAGATTAAAACA
genomic: CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
EST: gi|7145217|gb|AW506698.1|AW506698
EST:     CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG                         TTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
genomic: CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
EST: gi|211541851|gb|FL147713.1|FL147713
EST:     CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG                         TTTAAAGAAGACTGCAACACAGAGAAAAAGATTATTATAAAGATTAADACA
genomic: CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
EST: gi|32930164|gb|CF034976.1|CF034976
EST:     ACCAGAAGCAGTGTTATGAG                         TTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
genomic: ACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
EST: gi|32836690|gb|CD976368.1|CD976368
EST:     GTACCAGAAGCAGTGTTATGAG                         TTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
genomic: GTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
EST: gi|211153097|gb|FL147716.1|FL147716
EST:     CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG                         TTTAAAGAAGACTGCAACACAGAGAAAAAGATTATTATAAAGATTAAAACA
genomic: CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
EST: gi|78120827|gb|DV539211.1|DV539211
EST:     CAGTCCTTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG                         TTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA
genomic: CAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACA

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: 48 (upstream exon), 49 (downstream exon)
Score: 122

GAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 255

GAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 47

GAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

GAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAGgtaatgcaat ... acttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgatgcatgcaacttaatactcacatttttcttctttgttccacttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG
                    tactcac  putative branch site (score: 223)
                      ctcacatttttcttct  CT-rich tract
             aacttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcattgtccacccctcctatcagtttaagcttttgggttggactgattgatgcatgcaacttaatactcacatttttcttctttgttccacttgtatagTTTAAAGAAGATTGCAACACAGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA