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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACCTACTATTTGGGTAGTATCTTCTCTTCTTCCAATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaactatcactattatttgaatccaggcatggccaaactgaattttatagagtaggagcttctatttatagttttcttccttctgtgcatcttgt...

Basic information

species Zea mays
transcript GRMZM2G174107_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 5'ss of exon 4
CTACCTACTATTTGGGTAGTATCTTCTCTTCTTCCAATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaactatcactattatttgaatccaggcatggccaaactgaattttatagagtaggagcttc---tatttatagttttcttccttctgtgcatcttgt
 | |||||  |||||||  ||  ||| |||||||| |||||||||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| |  ||||| ||||||||||| || |    |||   | | | |  ||| |       |    ||||   | ||   |  |||| |||   |   
TTGCCTACAGTTTGGGTGATACTTTCACTTCTTCCGATTGTTGGTGGTGTAGCATTGGCATCTCTTACTGAGGCTTCCTTCAACTGgtatgtaacaagtactatcatttgaatccaagcttaataaaatgaactgtaaaggagcaattatgccaaacattttgggcttatgtgtttctctgctatt---
















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|32842413|gb|CD982094.1|CD982094
EST:     ATTGTTGGTGGTGATGCATTGGCATCTCTTACTGAGGCATCCTATAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|60351427|gb|DN218400.1|DN218400
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|13198536|gb|BG354370.1|BG354370
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|60354172|gb|DN221145.1|DN221145
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|32850209|gb|CD989890.1|CD989890
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|32841139|gb|CD980820.1|CD980820
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|16377738|gb|BI992093.1|BI992093
EST:     GCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCCTTCAATCCCGAAA
genomic: GCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|32840783|gb|CD980464.1|CD980464
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|13178610|gb|BG349868.1|BG349868
EST:     TTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCCTTCAATCCCGAAA
genomic: TTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|13558927|gb|BG550282.1|BG550282
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|32940452|gb|CF045271.1|CF045271
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|148937400|gb|EC881580.2|EC881580
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|15313742|gb|BI478935.1|BI478935
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|211517932|gb|FL479804.1|FL479804
EST:     GCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: GCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|148940598|gb|EC885404.2|EC885404
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|83279370|gb|DV943378.1|DV943378
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|56462047|gb|CK986345.1|CK986345
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|24934366|gb|CA452584.1|CA452584
EST:     ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: ATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
EST: gi|13126160|gb|BG316730.1|BG316730
EST:     GCATTGGCATCTCTTACTGAGGCATCCTTTAACTG                         GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA
genomic: GCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAA

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: 64

CTACCTACTATTTGGGTAGTATCTTCTCTTCTTCCAATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 674

CTACCTACTATTTGGGTAGTATCTTCTCTTCTTCCAATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 13

CTACCTACTATTTGGGTAGTATCTTCTCTTCTTCCAATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

CTACCTACTATTTGGGTAGTATCTTCTCTTCTTCCAATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaact ... atgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACCTACTATTTGGGTAGTATCTTCTCTTCTTCCAATTGTTGGTGGTGTTGCATTGGCATCTCTTACTGAGGCATCCTTTAACTGgtaagtaactatcactattatttgaatccaggcatggccaaactgaattttatagagtaggagcttctatttatagttttcttccttctgtgcatcttgt

- - - - - - - - - - - - - - - - - - - -  TGGTGG