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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAAGCTCTGGCTGAGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgctaatgcttttcatatccgtatcatcttgattatgcttgctttagtccacatcaacactcattcactcaaaacagtctacattattttttttc...

Basic information

species Zea mays
transcript GRMZM2G158872_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158872_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g43950.1 (Oryza sativa), 5'ss of exon 5
GCAAAAGCTCTGGCTGAGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgctaatgcttttcatatccgtatcatcttgattatgcttgctttagtccacatcaacactcattcactcaaaacagtctacattattttttttc--
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GCAAAAGCTCTGGCTGAGAAGAACGAACGGGATATGCAGGTTCAGAGGGAACAGGCAGAAAGAGACgtgagtgtca-tgttgtccatatacttgacagcttaatttttcttagttgaagtaa-atagtcttcattttcttctgatctatttatttcaattttttcatg
















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|6227229|gb|AW155828.1|AW155828
EST:     AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGAT                         AGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
genomic: AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
EST: gi|32863076|gb|CF002758.1|CF002758
EST:     GGAGCAGGCAGAGAGAGAT                         AGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGGAAA
genomic: GGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
EST: gi|5847361|gb|AW000440.1|AW000440
EST:     AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGAT                         AGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
genomic: AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
EST: gi|5860429|gb|AW011651.1|AW011651
EST:     AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGAT                         AGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
genomic: AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
EST: gi|5325205|gb|AI783396.1|AI783396
EST:     AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGAT                         AGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
genomic: AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
EST: gi|5895879|gb|AW037125.1|AW037125
EST:     AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGAT                         AGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA
genomic: AGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAA

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: 73

GCAAAAGCTCTGGCTGAGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAAGAGGGCAACTTGCGTGCTTTGTTATCAACTTTACAATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GCAAAAGCTCTGGCTGAGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAAGAGGGCAACTTGCGTGCTTTGTTATCAACTTTACAATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

GCAAAAGCTCTGGCTGAGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAAGAGGGCAACTTGCGTGCTTTGTTATCAACTTTACAATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GCAAAAGCTCTGGCTGAGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgcta ... tgaaatacagAGAATTGGAGACACTCTAGACTTCGAAATCAAGAGGTGGTCTGCTGGTAAAGAGGGCAACTTGCGTGCTTTGTTATCAACTTTACAATAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAAGCTCTGGCTGAGAAGAATGAACGTGATATGCAAGTTCAGAGGGAGCAGGCAGAGAGAGATgtaagtgctaatgcttttcatatccgtatcatcttgattatgcttgctttagtccacatcaacactcattcactcaaaacagtctacattattttttttc

- - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaacag