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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatccgattcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctctgcatatcattggtgaaaattgtgtatggtagattgttactaaattgttcagtttgctattcatcaatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT

Basic information

species Zea mays
transcript GRMZM2G550865_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G550865_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 19
gtgagatccgattcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctctgcatatcattggtgaaaattgtgtatggtagattgttactaaattgttcagtttgctattcatcaatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT---
|| | ||| |  |  | |   || ||| || ||| | | |  |    |  |      | | |   |     ||  ||  |  | | |||      |||||||||||| || ||  |||||||||| |    |||| ||||| |  || ||||| |||||   | |||||||||| ||||| |||||  | |||||||||||||  |||||||||   |||||||||||||| || ||||   
gttaaatctggattatttacgcacataaatatgc-tcagttttacctacctgctctgtataccaggt---ccaggggcaagcaatttgtgcatatgattgttactaactttttatgtttgctattgac---tcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAAC---CCTGAAGAAGCTGTCCATTGCTTTG
















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|67042557|gb|CO468812.1|CO468812
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
EST: gi|18963627|gb|BM660541.1|BM660541
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
EST: gi|19058178|gb|BM736845.1|BM736845
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
EST: gi|87152018|gb|DY396807.1|DY396807
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
EST: gi|32858467|gb|CD998148.1|CD998148
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
EST: gi|67032677|gb|CO461426.1|CO461426
EST:     CTGGAAATGGTCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
EST: gi|87157645|gb|DY402434.1|DY402434
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAG                         GCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG
EST: gi|26558945|gb|CA831180.1|CA831180
EST:     CTGTTCATCTACTCTGGAAATGGCCACGCAG-GATCGGAATTCTGGAAAG                         GCAAGCGCGAG-GTGTCTCCCACACTATGGCAACCACCAAG-GGCATTTTG
genomic: CTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTG

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), 47 (downstream exon)
Score: 405

ATTGATTTACACAAATTCTGGTCTTGCTATCTTGGCTTTAACTTCAAGTGCTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 239

ATTGATTTACACAAATTCTGGTCTTGCTATCTTGGCTTTAACTTCAAGTGCTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

ATTGATTTACACAAATTCTGGTCTTGCTATCTTGGCTTTAACTTCAAGTGCTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

ATTGATTTACACAAATTCTGGTCTTGCTATCTTGGCTTTAACTTCAAGTGCTGTTCATCTACTCTGGAAATGGCCACGCAGTGATCGGAATTCTGGAAAGgtgagatccg ... aatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtatggtagattgttactaaattgttcagtttgctattcatcaatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT
                 tactaaa  putative branch site (score: 301)
            attgttactaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatccgattcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctctgcatatcattggtgaaaattgtgtatggtagattgttactaaattgttcagtttgctattcatcaatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT