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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaaagtgcctgaattttttgaagcttgggcatatttcatgagatgttaacattgattcaaatgatttaatacaacttttgtag

Basic information

species Zea mays
transcript GRMZM2G365035_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G365035_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g22710.1 (Oryza sativa), 5'ss of exon 8
AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaaagtgcctgaattttttgaagcttgggcatatttcatga-gatgttaacattgattcaaatgatttaatacaacttttgtag
|||||||||| |||||||||| |||||  | |||||||| |||||||||||||||||||||||||| ||||||||||| || ||||||||||||||| ||||||||||  |   | | | ||    ||| |||   |||   ||| || ||| |     |  |||  ||   ||||   || || ||||||
AGAAGGAGGACAGGCATCTGATATACCTCTAGATATATCTGTATTACATAATATGCGTCAGTTTGTAAAATACAGTCGGTTTAAGCAATTTGCTTTACGGgtaagttatcataccataacttaagggaatcttatccatgactcaggatgatttcggagtcaattttaaatgttta---catctcttgtag

upper sequence: GRMZM2G365035_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 10
AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaaagtgcctgaattttttgaagcttg--ggcat--atttcatgagatgttaacattgattcaaa--tgatt--taatacaacttttgtag--
|||||||||| | ||||  || || ||  | |||||||| ||  |    || ||||| |||||||||||||| ||||| ||||| ||||||||  | ||||||||  |||        |   |||| | |   |  |||||  |     |  |||||  |  ||  || | |  |||||  |  |  ||  | || |   
AGAAGGAGGAGAAGCATTGGAGATTCCTATTGATATATCTGTCCTGAGCAACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGGgtaagagaaattaattctagccttttcaggtcagaaggcatggaacctgtttgatgtccagctttttttataattgattactgttggaatatatggaaat

upper sequence: GRMZM2G365035_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G66210.2 (Arabidopsis thaliana), 5'ss of exon 9
AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaaagtgcctgaattttttgaagcttgggcatatttcatgagatgttaacattgattcaaatgatttaatacaacttttg-tag
|||||| || || ||  |||| || ||  | || || |||||  |  | ||  |  | || ||||||| |||||| ||| | |||||||||||||||||||||||||||| | |   ||| || ||| |   |||  | |    | | |||    |||| |  || |||| |||    |  ||| ||  ||
AGAAGGCGGGAATGCTACTGATATCCCTGTCGACATTTCAGTTCTGAACAACTTAAGACAATTTGTGAGATACAGCCGTCTAAAGCAATTTGCTTTAAGGgtaagttaaatgag---gaagttgttgga---tggataaaaacaaagtgatccggacat-gtctctaatgctttgtgtctccttctggcag

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|149087834|gb|EE287144.2|EE287144
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|32840606|gb|CD980287.1|CD980287
EST:     ATATGAGTCAGGTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTGAACTCAGAAGAGATGTCCGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|76017952|gb|DT945122.1|DT945122
EST:     AGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: AGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|149043308|gb|EE047371.2|EE047371
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|60345110|gb|DN212083.1|DN212083
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|211516679|gb|FL422119.1|FL422119
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|76284446|gb|DV024014.1|DV024014
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|87153749|gb|DY398538.1|DY398538
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCCGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|32935092|gb|CF039904.1|CF039904
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATNTGCTTTAAGG                         GCATTAGCATCTACATTGAACTCAGAAGAGATGTCCGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|37388728|gb|CF631576.1|CF631576
EST:     TTGCNTTTAAGG                         GCATTAGCATCTACA-TAAACTTCAGAAGAGATGTCTGATCTTCGTGATC
genomic: TTGC-TTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAAC-TCAGAAGAGATGTCTGATCTTCGTGATC
EST: gi|33091766|gb|CF051760.1|CF051760
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTGAACTCAGAAGAGATGTCCGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|32840607|gb|CD980288.1|CD980288
EST:     GTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTGANCTCAGAAGAGATGTCCGATCTTCGTGATCAA
genomic: GTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|45567561|gb|CK985631.1|CK985631
EST:     ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: ATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
EST: gi|149102041|gb|EE188040.2|EE188040
EST:     AGTCGTTTCAAGCAATTTGCTTTAAGG                         GCATTAGCATCTCCATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA
genomic: AGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAA

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: 101

AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAAC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 97

AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 78

AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaa ... acttttgtagGCATTAGCATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGGAGGAAAGGCATCTGAAATACCCTTGGATATATCAGTATTACATAATATGCGTCAGTTTGTGAAATACAGTCGTTTCAAGCAATTTGCTTTAAGGgtaagttaaaagtgcctgaattttttgaagcttgggcatatttcatgagatgttaacattgattcaaatgatttaatacaacttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA