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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttcgtcaataagcactacaacatttaagtttatcatccatttcaaattttattttgaattctgatagctggtttgattggggcaacaacaatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 8
ctttcgtcaataagcactacaacatttaagttt-atcatccatttcaa--attttattttgaattctgatagctggtttgattggggcaacaacaatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG
  ||   ||| |     |  |||||| ||| || ||||| ||||  ||  || || |||     |       ||| | ||||  | ||||| |||||||||||||  ||||||||||||| |||||||||||||| |||||| |||| ||||| ||||||||||||||||||||||||||||||||||| |||||||| || |
--ttgcacaaaatctgtttgaacattgaagcttgatcattcattagaaaaatattttttctctgttgagctactgatatgat-agagcaacgacaatttgtagGGGATTGGCTCTCCTGTATTTGACAAACTTGAGGCTGAATTGGCGAAAGCTATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATCGGCAGTGGATTTG
















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|149088514|gb|EE177624.2|EE177624
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTT
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTT
EST: gi|211540751|gb|FL105309.1|FL105309
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|32929391|gb|CF034203.1|CF034203
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAGCGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|60357187|gb|DN224160.1|DN224160
EST:     CATGCATTGCAAGAAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: CATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|40335508|gb|CK369578.1|CK369578
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|213172541|gb|FM189510.1|FM189510
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAACGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|32808278|gb|CD960512.1|CD960512
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAACGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|113701263|gb|EE678767.1|EE678767
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAGGAAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|32808708|gb|CD960942.1|CD960942
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAACGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|18659504|gb|BM500373.1|BM500373
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAACGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|37385128|gb|CF629683.1|CF629683
EST:     AAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: AAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|32929474|gb|CF034286.1|CF034286
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAACGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|67042195|gb|CO468450.1|CO468450
EST:     GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGT                         GGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
EST: gi|32793479|gb|CD945715.1|CD945715
EST:     GAGATTCAATTGGTGGAGTCGTCACATGCATTGCAAGAAACGTTCCTCGT                         GGTCTTGGCTCTACTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC
genomic: GAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCC

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: 193

AGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 543

AGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 564

AGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 457

AGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttg ... caatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattttattttgaattctgatagctggtttgattggggcaacaacaatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG
     ttattttgaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttcgtcaataagcactacaacatttaagtttatcatccatttcaaattttattttgaattctgatagctggtttgattggggcaacaacaatttgtagGGTCTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - -gcactac
- - - - - - - - - - - - - - - - - -catccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctggtt