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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtcgccctgctcatttatctcgtggatgacttgaaaaaaaacgaggtttggattctgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG

Basic information

species Zea mays
transcript GRMZM2G026470_T01
intron # 6
splice site 3'
intron type U2

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|71331881|gb|DR802819.1|DR802819
EST:     ACGACTTTCTGCCCCGCGGC-GCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTA
genomic: ACGACTTCCTGCCC-GCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTA
EST: gi|78023075|gb|DV491462.1|DV491462
EST:     AATGACTTCTTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
EST: gi|28984521|gb|BQ539133.2|BQ539133
EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
EST: gi|71331880|gb|DR802818.1|DR802818
EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
EST: gi|62550248|gb|DN830668.1|DN830668
EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGT-TC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
EST: gi|78121801|gb|DV540185.1|DV540185
EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGGGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
EST: gi|84908555|gb|DW404433.1|DW404433
EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGT-TC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
EST: gi|5499294|gb|AI855161.1|AI855161
EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
EST: gi|60354156|gb|DN221129.1|DN221129
EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

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), 40 (downstream exon)
Score: 15

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 362

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG
                    tgttgac  putative branch site (score: 41)
                                        cttctgt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtcgccctgctcatttatctcgtggatgacttgaaaaaaaacgaggtttggattctgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA