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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaattttcctgtgatgttgattggtctcccgttggtttcgatctatgcagaag

Basic information

species Zea mays
transcript GRMZM2G044137_T02
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|149089950|gb|EE179239.2|EE179239
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|211067927|gb|FL140853.1|FL140853
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|60355557|gb|DN222530.1|DN222530
EST:     CATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|60394375|gb|DN227245.1|DN227245
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|9824981|gb|BE575183.1|BE575183
EST:     GTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGC
genomic: GTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGC
EST: gi|60338522|gb|DN205495.1|DN205495
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|15100298|gb|BI396089.1|BI396089
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|89251915|gb|DY623701.1|DY623701
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|31406277|gb|CD485009.1|CD485009
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|31441073|gb|CD510504.1|CD510504
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|211067924|gb|FL140850.1|FL140850
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|60347030|gb|DN214003.1|DN214003
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|67023955|gb|CO452704.1|CO452704
EST:     CCCATCGCCGCCAGTGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|60341097|gb|DN208070.1|DN208070
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|27575973|gb|CA998667.1|CA998667
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|76013092|gb|DT940262.1|DT940262
EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|211065202|gb|FL140848.1|FL140848
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|211065201|gb|FL140847.1|FL140847
EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga
EST: gi|60357629|gb|DN224602.1|DN224602
EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

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: 57

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 34

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 31

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaattttcctgtgatgttgattggtctcccgttggtttcgatctatgcagaag

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