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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgctgagtctcatgttcacctctcctgcgtgattgttatgcatggttatggatgtagtagcagctgtactctagaaaccggacaagaatgccct...

Basic information

species Zea mays
transcript GRMZM2G180246_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180246_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g52320.1 (Oryza sativa), 5'ss of exon 2
TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgctgagtctcatgttcacctctcctgcgtgattgttatgcatggt-tatggatgtagtagcagctgtactctagaaaccggacaagaatgccct----
|| ||||| ||||||||||||||||||||||||||||| ||||||||||||||||| |||| ||| |||||||  |||||||||  |||   | || | |  || |  |    || || | || |   | |   | ||  ||     |||||   |     |    ||   ||| | |    
TATCTGGATGAGAACAAGCAGCTGATCCTGGCCATCCTTGACAACCAGAACAATGGGAAGGTGGAAGAGTGCGCTCGgtgagtt--tgatcttgatctcc--ctgttatcatggagtgctgtgaaaactctgaagttgctgttctttctgtagcttttgctctat-cagagatgtcttgttt

upper sequence: GRMZM2G180246_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S1_784V6.1 (Physcomitrella patens), 5'ss of exon 2
TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgctgagtctcatgttcacctctcctgcgtgattgttatgcatggttatgga--tgtagtagca-gctgtactctagaaaccggacaagaatgccct-----
|||||||||||||||||||||||||| || || || ||||| || || |||  ||| |||  | | || || |    ||  ||| || | | || |   ||| | |         ||| || | || |||    |  || | ||  | |||    |   |  ||    ||   ||  | |     
TACCTGGACGAGAACAAGCAGCTGATTCTCGCAATTCTCGATAATCAAAACCTTGGAAAGCTGAACGAATGTGCTACgtacgtttctaattttcgt---cacattt----taaagttggta-gaatagttgcaaacctgcattacgatgctacgatgcggggactattcatccatcgcttggtaa

upper sequence: GRMZM2G180246_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ18273 (Selaginella moellendorffii), 5'ss of exon 2
TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgctgagtc---------tcatgttcacctctc---ctgcgtgattgttatgcatgg---ttatggatgtagt--agcagctgtactctagaaaccggacaagaatgccct------------------------------------------
||| ||||||||||||||||||| || || || ||||| ||||||||||||   ||||||    | || ||||  | ||  |   |||| ||           || | | ||||||   | |  || ||  ||| |       || |  || |  |  |||  |||   |||       |   || |  |   |                                          
TACTTGGACGAGAACAAGCAGCTCATACTTGCAATCCTTGACAACCAGAACCTCGGCAAGCTTAATGAATGCGCGCAgtatgccactgactcgaaaatcttcgatctccccctctctctccggctggtttctattcgaatctcttcttcatttctttaagcttctgccttctttcgctggatgaacaccgaattcatggaaggtggaacttaattcttccctgctttctctttcag

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|93015153|gb|EB640673.1|EB640673
EST:     GCAAGGCGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: GCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|71417542|gb|DR804109.1|DR804109
EST:     GAACAATGGCAAGGCGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTTCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: GAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|211135406|gb|FL464567.1|FL464567
EST:     CAATGGCAAGGCGGAGGAGTGCGAAC-                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTANCTGGCNGCCATCGCTGA
genomic: CAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|31558279|gb|CD527491.1|CD527491
EST:     GGCCATCCTCGACAACCATGAACAATGGCAAGGCTGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: GGCCATCCTCGACAACCA-GAACAATGGCAAGGC-GGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|14245547|gb|BG874129.1|BG874129
EST:     CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|20802701|gb|BQ293751.1|BQ293751
EST:     CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|31405520|gb|CD484252.1|CD484252
EST:     CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|60394771|gb|DN227641.1|DN227641
EST:     CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
EST: gi|31558313|gb|CD527525.1|CD527525
EST:     CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACG                         GCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA
genomic: CTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGA

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: 1202

TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGACAGCCAGCCGCCACAGACCGCGCCACTATCACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 37

TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGACAGCCAGCCGCCACAGACCGCGCCACTATCACAG


Block sizes: 44 (upstream exon), 31 (downstream exon)
Score: 6

TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGACAGCCAGCCGCCACAGACCGCGCCACTATCACAG


Block sizes: 39 (upstream exon), 41 (downstream exon)
Score: 12

TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgct ... tgtcttgcagGCACCAAGCTAAGCTCCAGCACAACCTCATGTACCTGGCCGCCATCGCTGACAGCCAGCCGCCACAGACCGCGCCACTATCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACGgtgagttgctgagtctcatgttcacctctcctgcgtgattgttatgcatggttatggatgtagtagcagctgtactctagaaaccggacaagaatgccct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG