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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGGCCGAGTCGCAGCGGCAGGCGGACCTACTCAAGCAGGAGGGCAACGCCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctgactgactccccgctcccggcggccaggatcatcggcctgcttcgcgtgttgcgcgcttgctgtcccaagtagttacgtgcgcgtcatttcc...

Basic information

species Zea mays
transcript GRMZM2G104769_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104769_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g02140.3 (Oryza sativa), 5'ss of exon 1
CGGGGCCGAGTCGCAGCGGCAGGCGGACCTACTCAAGCAGGAGGGCAACGCCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaag--cctgactgactccccgctcccggcggccaggatcatcggcctgcttcgcgtgttgcg-cgcttgctgtcc-caagtagttacgtgcgcgtcatttcc
| | || | |||| ||||||||||||| || ||||||||||||||||||||||| |||| |||||| ||| ||||||||||||||||||||||||||||||||||   |   | |   |  ||| | ||  |    |   | ||    | |||||       |  |  |||    |  || |  |   ||      |||     
CAGCGCGGCGTCGAAGCGGCAGGCGGAGCTGCTCAAGCAGGAGGGCAACGCCTTCTTCAAGAAGGACCGCATCAGCGCCGCCATCGACGCCTACACCGGGgtaaggttcccgccgtggcatcgcccgcg-tgattcgtgccgtcctaattcttcgaaccaaccaacatttggacccttcaggccgccccgc-tatatcagca--
















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|76913822|gb|DV165266.1|DV165266
EST:     CCTTTTTCAGGAAGGAACGCCTCACCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|211321471|gb|FL171489.1|FL171489
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCGTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTNGGACCAACCGAGCACT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATT-GGACCAACCGAGCACT
EST: gi|211321469|gb|FL171487.1|FL171487
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|211321468|gb|FL171486.1|FL171486
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATAT-GGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|211321470|gb|FL171488.1|FL171488
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCGTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATAT-GGASCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|94476727|gb|EB705685.1|EB705685
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|211196887|gb|FL171483.1|FL171483
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|61119637|gb|DN560598.1|DN560598
EST:     AGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: AGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|211321467|gb|FL171485.1|FL171485
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|211321466|gb|FL171484.1|FL171484
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|149106376|gb|EE292096.2|EE292096
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
EST: gi|91054321|gb|EB164739.1|EB164739
EST:     CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGG                         GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT
genomic: CCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTT

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), 47 (downstream exon)
Score: 57

CGGGGCCGAGTCGCAGCGGCAGGCGGACCTACTCAAGCAGGAGGGCAACGCCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 140

CGGGGCCGAGTCGCAGCGGCAGGCGGACCTACTCAAGCAGGAGGGCAACGCCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CGGGGCCGAGTCGCAGCGGCAGGCGGACCTACTCAAGCAGGAGGGCAACGCCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 45

CGGGGCCGAGTCGCAGCGGCAGGCGGACCTACTCAAGCAGGAGGGCAACGCCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctga ... tggttgacagGCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGGCCGAGTCGCAGCGGCAGGCGGACCTACTCAAGCAGGAGGGCAACGCCTTTTTCAGGAAGGAACGCCTCAGCGCCGCCATCGACGCCTACACCGGGgtaagcctgactgactccccgctcccggcggccaggatcatcggcctgcttcgcgtgttgcgcgcttgctgtcccaagtagttacgtgcgcgtcatttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccccgc