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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaatagattttcgtgcattgcattatcagatttataagttaaataatctgttcaataactttcagcaacctctgctaacggcttttgacgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG

Basic information

species Zea mays
transcript GRMZM2G052880_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 14
----tacaatagattttcgtgcattgcattatcagatttataagttaaataatctgttcaataactttcagcaacctctgctaacggcttttgacgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG
     |||| |||   |  | ||   | ||  ||  | | ||  | ||  |  |||||      | ||||    | | |    | |  | | ||   ||| ||||||||| ||| |||||||| | || ||||||||||  || |||||||||||||||||||| ||||| || || || || ||||| || |||
ttggaacaagagaagctattccacaccgtttgcatttgtgtacat-aacca--ctgtttgtcttccttcacgggcatataacta-gtatatggaaaatttgcagTGATTCAGTGCTGAAGCATTCGTCGAGTGACTTCAAAAAGCTTGGTCAGCGTATATTTGTGTTTGTCATTGGTGGCGCCACTCGGTCGGAG
















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|67022604|gb|CO451353.1|CO451353
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTNCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|60345833|gb|DN212806.1|DN212806
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|60398850|gb|DN231666.1|DN231666
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|211539100|gb|FL044736.1|FL044736
EST:     ACAGGTGGCACATGGGCAAGACCYCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCMTGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|50336914|gb|CO532040.1|CO532040
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|76911270|gb|DV164216.1|DV164216
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|6827451|gb|AW331094.1|AW331094
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|76908403|gb|DV162923.1|DV162923
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|6194629|gb|AW146733.1|AW146733
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
EST: gi|211447144|gb|FL470093.1|FL470093
EST:     ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAG                         TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG
genomic: ACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCG

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: 47 (upstream exon), 49 (downstream exon)
Score: 97

CCAGTAGCTCTGCCCGAACAAGCCCCGCTCACTCAATGCGATCCAGACGAACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

CCAGTAGCTCTGCCCGAACAAGCCCCGCTCACTCAATGCGATCCAGACGAACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

CCAGTAGCTCTGCCCGAACAAGCCCCGCTCACTCAATGCGATCCAGACGAACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 92

CCAGTAGCTCTGCCCGAACAAGCCCCGCTCACTCAATGCGATCCAGACGAACAGGTGGCACATGGGCAAGACCTCGTGGCTCTGATGATGGATATTCAAGgtgagtggtg ... cgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatctgttcaataactttcagcaacctctgctaacggcttttgacgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG
                                             cgttttcc  CT-rich tract
          aataacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaatagattttcgtgcattgcattatcagatttataagttaaataatctgttcaataactttcagcaacctctgctaacggcttttgacgttttccagTGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG

- - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttttg