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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgccctgttgccctgctttccctgattccattacctccctaatctagaacgttcgagtagatctgggggttggtttgtcgcgcggttcctgtgtttttgtggagattttttacttttacctgtgtgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA

Basic information

species Zea mays
transcript GRMZM2G028096_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028096_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 3'ss of exon 1
gtacgtgccctgt--tgccctgctttccctgattccattacctccctaatctagaacgttcgagtagatctgg-gggttggtttgtcgcgcggttcctgtgtttttgtggagattttttacttttacctgtgtgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA
|| ||| ||| ||  | | ||   | ||||     |    || ||     ||| | |   | | |  |||    || || | || ||||| || |  ||||    || |  |   ||||  ||||           |||||||||||||||||||| || ||||||||| ||||||||||||| |||||||| ||
gtgcgttccccgtgctactctcgatcccctcgcggcggagccccctc---ctatatc--cccactccatccatcggattcggttatcgcgtggctgatgtgcgcctgcgttg---ttttgttttt-----------ttgcagAAGATGGACATGGGGCCATGCCCGAAGATGCACTCGCTGCAGCTGCGCAAGGA
















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|211342903|gb|FL126052.1|FL126052
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342904|gb|FL126053.1|FL126053
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342898|gb|FL126047.1|FL126047
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342902|gb|FL126051.1|FL126051
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211340511|gb|FL126040.1|FL126040
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342905|gb|FL126054.1|FL126054
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342900|gb|FL126049.1|FL126049
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|71764556|gb|DR962493.1|DR962493
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|74232160|gb|DT640074.1|DT640074
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342892|gb|FL126041.1|FL126041
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGTTTACC                         AGGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAG-ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAA
EST: gi|211340509|gb|FL126038.1|FL126038
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211345283|gb|FL126056.1|FL126056
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTG
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTG
EST: gi|211342897|gb|FL126046.1|FL126046
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342893|gb|FL126042.1|FL126042
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342896|gb|FL126045.1|FL126045
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211340507|gb|FL126036.1|FL126036
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
EST: gi|211342894|gb|FL126043.1|FL126043
EST:     GCCGCCTCTACCTCGCCGGSCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGGCCGTGCC-GAAGCTGCACTCGCTGC
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGC
EST: gi|211340508|gb|FL126037.1|FL126037
EST:     GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACC                         AAGATGGACATGGGCCCGTGCC-GAAGCTGCACTC
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTC
EST: gi|211340510|gb|FL126039.1|FL126039
EST:     GCCGCCTCTACCTCGCCGGCCTCTGNCCCCACGACCTCTTCCAGNTTACC                         AGGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA
genomic: GCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 155

CAACGGCGATGTACGGGAGGTCAGCCGCAAGTACTATGATCGCGACGTCTGCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 62

CAACGGCGATGTACGGGAGGTCAGCCGCAAGTACTATGATCGCGACGTCTGCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

CAACGGCGATGTACGGGAGGTCAGCCGCAAGTACTATGATCGCGACGTCTGCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

CAACGGCGATGTACGGGAGGTCAGCCGCAAGTACTATGATCGCGACGTCTGCCGCCTCTACCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTTACCgtacgtgccc ... tgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgcggttcctgtgtttttgtggagattttttacttttacctgtgtgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA
                       agattttttactttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgccctgttgccctgctttccctgattccattacctccctaatctagaacgttcgagtagatctgggggttggtttgtcgcgcggttcctgtgtttttgtggagattttttacttttacctgtgtgttttgcagAAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG