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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaattttcctgtgatgttgattggtctcccgttggtttcgatctatgcag

Basic information

species Zea mays
transcript GRMZM2G044137_T01
intron # 1
splice site 5'
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|76013092|gb|DT940262.1|DT940262
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|211065202|gb|FL140848.1|FL140848
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|31406277|gb|CD485009.1|CD485009
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|166647094|gb|EG316502.1|EG316502
EST:     CGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|91049094|gb|EB159512.1|EB159512
EST:     TCCATTGCCGCCAGTGTCTGTTTGATCCGATGGCTCCCCCGAAGAAGTTG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|60394375|gb|DN227245.1|DN227245
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|60355557|gb|DN222530.1|DN222530
EST:     CATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|211067927|gb|FL140853.1|FL140853
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|67023955|gb|CO452704.1|CO452704
EST:     CCCATCGCCGCCAGTGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|149089950|gb|EE179239.2|EE179239
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|32914523|gb|CF019335.1|CF019335
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGTTTTTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|32865422|gb|CF005104.1|CF005104
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|60338522|gb|DN205495.1|DN205495
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|15100298|gb|BI396089.1|BI396089
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|9824981|gb|BE575183.1|BE575183
EST:     GTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC-                         --GAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|211067924|gb|FL140850.1|FL140850
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|89251915|gb|DY623701.1|DY623701
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|27575973|gb|CA998667.1|CA998667
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|31441073|gb|CD510504.1|CD510504
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|60357629|gb|DN224602.1|DN224602
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|211065201|gb|FL140847.1|FL140847
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|60341097|gb|DN208070.1|DN208070
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|166473228|gb|EG321222.1|EG321222
EST:     CGAAGAAGTCG                         AAGAAGAGCACAGAAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAG
genomic: CGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAG-AGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAG
EST: gi|60347030|gb|DN214003.1|DN214003
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGC

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), 49 (downstream exon)
Score: 692

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 481

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 374

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 432

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... atctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaattttcctgtgatgttgattggtctcccgttggtttcgatctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT