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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattcttgtgtacttctttgggcgagatggacaggtctggtgcagtggtgagaagccttcatactgagccaaaggtcctgtgtttg...

Basic information

species Zea mays
transcript GRMZM2G420865_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 5'ss of exon 15
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattct-tgtgtacttctttgg-gcgagatggacaggt-ctggtgcagtggtgagaagccttcatactgagccaaaggtcctgtgtttg
||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||| | ||| |||||||||||||||   || |||||||||||     || ||||| | | | || |||||||  || | || | ||  | |   ||||      ||   |  ||| | || |||    | |   ||  ||
AGAAAATATGATAGCTCATAAGGATGAGATATACTCAAGACCAAAGAGAACCTGGTTTGCTACTGAGAAGGAAAAGAAACTTTTGGCAAAGGCTGCTAAAgtaagttcgccttaaattgtatatatatttctttgatgccaaattgccaattacatatgcaaattctag---ctctcaaattgtgcctgctgcctgctgcatg

upper sequence: GRMZM2G420865_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 5'ss of exon 15
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattcttgtgtacttctttgggcgagatggacaggtctggtgcagtggtgagaagccttcatac-tgagccaaaggtcctgtgtttg
 ||||| ||||| || ||||||||||| || |||||||| || || |||||||||||||| || |||| |||||||||   | |||||   || || || ||||    || |   |   |||| |  || ||||       | |  ||      |  | || ||   |   ||  |   ||||       | |  | ||  
TGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAAAGgtaatttcatattgcaccattgt-tgtttatttgtattcatttgtaagtctatatataatgttgtatatgttttgtctgtgagttggcatttccatattct
















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|78027541|gb|DV495928.1|DV495928
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|211352888|gb|FL146172.1|FL146172
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAAGAA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAA-GAA
EST: gi|211352883|gb|FL146167.1|FL146167
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGT
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGT
EST: gi|4887454|gb|AI677553.1|AI677553
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTCCTAA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAA
EST: gi|31349040|gb|CD433397.1|CD433397
EST:     CCTGGCTTGCTACTGAAAGGGAGAATAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGA
EST: gi|211352887|gb|FL146171.1|FL146171
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCA
EST: gi|211352885|gb|FL146169.1|FL146169
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|4887453|gb|AI677552.1|AI677552
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGAT
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGAT
EST: gi|33100275|gb|CF060235.1|CF060235
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGT
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGT
EST: gi|78090029|gb|DV518403.1|DV518403
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGG

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: 114

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 56

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattcttgtgtacttctttgggcgagatggacaggtctggtgcagtggtgagaagccttcatactgagccaaaggtcctgtgtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA