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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcagctcttactgaaaacatggtgctcacatgtgcttgtacatcagtgcatctatgcaatgttttaagaataattcttttccctgtgcacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCACATCGAGGATCATCCTGATCATCTACTGGAGGCTCTACAAGAAGCCATGT

Basic information

species Zea mays
transcript GRMZM5G864166_T01
intron # 10
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|211233119|gb|FL455320.1|FL455320
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|76293254|gb|DV032822.1|DV032822
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|50335339|gb|CO530465.1|CO530465
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|78088236|gb|DV516629.1|DV516629
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|60340733|gb|DN207706.1|DN207706
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|32828888|gb|CD968566.1|CD968566
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCGC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|71756436|gb|DR954373.1|DR954373
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|50329288|gb|CO524414.1|CO524414
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|86469098|gb|DY235468.1|DY235468
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|71428088|gb|DR809138.1|DR809138
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|33100222|gb|CF060182.1|CF060182
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCGC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|50326456|gb|CO521582.1|CO521582
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC
EST: gi|32829465|gb|CD969143.1|CD969143
EST:     CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAG                         ATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCGC
genomic: CTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCAC

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), 48 (downstream exon)
Score: 62

CCAATCATCAAATTGGAATTCAGGGACCGCAACCTCTGAAATGGCCAGTTCTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCACATCGAGGATCATCCTGATCATCTACTGGAGGCTCTACAAGAAGCCATGT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 47

CCAATCATCAAATTGGAATTCAGGGACCGCAACCTCTGAAATGGCCAGTTCTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCACATCGAGGATCATCCTGATCATCTACTGGAGGCTCTACAAGAAGCCATGT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 20

CCAATCATCAAATTGGAATTCAGGGACCGCAACCTCTGAAATGGCCAGTTCTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCACATCGAGGATCATCCTGATCATCTACTGGAGGCTCTACAAGAAGCCATGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 37

CCAATCATCAAATTGGAATTCAGGGACCGCAACCTCTGAAATGGCCAGTTCTCACCAAGCTTTAATAGGAGGGATTGCTTATGGTGGCTATGCTCGCAAGgtttgaacta ... cacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCACATCGAGGATCATCCTGATCATCTACTGGAGGCTCTACAAGAAGCCATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtgcatctatgcaatgttttaagaataattcttttccctgtgcacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCACATCGAGGATCATCCTGATCATCTACTGGAGGCTCTACAAGAAGCCATGT
                               ttcttttccctgtgc  CT-rich tract
               aatgttttaagaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattcagctcttactgaaaacatggtgctcacatgtgcttgtacatcagtgcatctatgcaatgttttaagaataattcttttccctgtgcacatcgcagATCGTTGGACGGGTTTTGCGCAAAATACCAGAACAGTTTGGCCGTGTGCACATCGAGGATCATCCTGATCATCTACTGGAGGCTCTACAAGAAGCCATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- ttcagct
- - - - -cttactg
- - - - - - - - - - - tggtgct
- - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - gtgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaataa