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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaatatcaattttctgaatataaattttatgctgtcattgcttttctattaagatatggtactgtgtccctacctcgttcatgccctatgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT

Basic information

species Zea mays
transcript GRMZM5G871463_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871463_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 3'ss of exon 2
aaaaatatcaattttctgaatataaattttatgctgtcattgcttttcta---ttaagatatggtactgtgtccctacctcgttcatgccctatgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT
    |||   |      ||   |    |||    | | | |   ||| ||   || | || |     |  |  ||| |||  || |   |  |   |||||||||| ||||| || ||  ||   ||||| ||||| ||||||||||| |||||||||||||| |||||||| ||| |||| ||||| ||| ||||||||| |
---tatacatacaaagagatattgtcctttgcattttaaatttctttatatgcttcaaatgttacttttggctcctgccttatttagatctaactgtatgcagGTTTCATCCTTCATGCATGAGCATGACGATTGAGCAGGCCAAAAAACTAGATCACTTTGTGTGCTCAGATTGTGTCAAGGAAAACGGTGCAAAGAGACCT
















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|211293088|gb|FL433983.1|FL433983
EST:     CGGTACAACCCGGATGACCTCATGGTGCAGTGGGAGGCTTGCAAGCACTG                         GTTCCATCCTTCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
EST: gi|26456797|gb|CA828380.1|CA828380
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAAGCTAG
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAA-GCTAG
EST: gi|37376233|gb|CF624624.1|CF624624
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
EST: gi|37379451|gb|CF626469.1|CF626469
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
EST: gi|60355176|gb|DN222149.1|DN222149
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
EST: gi|211377790|gb|FL432886.1|FL432886
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
EST: gi|211492877|gb|FL137487.1|FL137487
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTG
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTG
EST: gi|78544163|gb|DV621661.1|DV621661
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
EST: gi|40334533|gb|CK368603.1|CK368603
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
EST: gi|5152847|gb|AI759012.1|AI759012
EST:     CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG                         GTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA
genomic: CCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGA

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), 48 (downstream exon)
Score: 223

GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 71

GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 98

GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 95

GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTGgtacatttgt ... tgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctattaagatatggtactgtgtccctacctcgttcatgccctatgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT
     ttaagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaatatcaattttctgaatataaattttatgctgtcattgcttttctattaagatatggtactgtgtccctacctcgttcatgccctatgatatgcagGTTCCATCCATCTTGTGTGGCTATGACCATTGAACAGGCCAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA