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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttggctccttgacatatcattcttttatattaggttagagacataattttttcagcaagagattcaggaggaacgttgatattattatgctttcctttggaatgtcatcatctgccgaagtctcccattcttgtcggtgactttacacattgctttgcttggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC

Basic information

species Zea mays
transcript GRMZM2G001850_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001850_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g52960.1 (Oryza sativa), 3'ss of exon 18
gttagttggctccttgacatatcattcttttatattaggttagagacataattttttcagcaagagattcaggaggaacgttgatattattatgctttcctttggaatgtcatcatctgccgaagtctc--ccattcttgtcggtgactttacacattgctttgcttggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC
               | ||  |   ||| |||  ||   ||| | |||| |   |||  |  |  |      | |||||    | | |||| |  |    ||||  |   |  ||  ||  | || |    | ||| | |||  |||| |    | ||||||  | || |  |||| |||||||||||||||||   ||||   | |||||||   |||||||||||  |||||||| | ||||| ||||| |||||||||||||| |||||||| 
---------------gtcagttgcctctgttacgtttattta-acacattacacttt--gttaatgccctttgcggaac----acagtattctcttcgtttttg--acccctgcacttggtgtagccctatctattatcgtcactgacatgtggc-ttgctt--cctgat--gcagGATGGCGTACATGGATTTTGCGGACAACGGTTCCTTGTCGAAAGCATACGAACTGAATGGATCTGACCTCGGTGGATACAGCTTGTATGTTGATGAAGCG
















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|60352099|gb|DN219072.1|DN219072
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|211390614|gb|FL418023.1|FL418023
EST:     ATCACTCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|78076793|gb|DV505227.1|DV505227
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|71327897|gb|DR800580.1|DR800580
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|37386475|gb|CF630423.1|CF630423
EST:     ATCACTCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|60355101|gb|DN222074.1|DN222074
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|78076792|gb|DV505226.1|DV505226
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|61118398|gb|DN559359.1|DN559359
EST:     ATCACTCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|161587809|gb|EY961736.1|EY961736
EST:     CGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: CGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|32850141|gb|CD989822.1|CD989822
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|149045940|gb|EE047938.2|EE047938
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|61118397|gb|DN559358.1|DN559358
EST:     ATCACTCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|211355109|gb|FL475414.1|FL475414
EST:     CAATTCCAAA-GATTTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: CAATTCCAAAGGA-TTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|211324531|gb|FL445883.1|FL445883
EST:     AAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: AAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|211449697|gb|FL381429.1|FL381429
EST:     ATCACTCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|211039114|gb|FL370414.1|FL370414
EST:     ATCACTCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTTCCTTGAATAAAGCATACG
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATT-CCTTGAATAAAGCATACG
EST: gi|6021892|gb|AW066820.1|AW066820
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|60400636|gb|DN233443.1|DN233443
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
EST: gi|110480718|gb|EE010818.1|EE010818
EST:     ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG                         AATGGGGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA
genomic: ATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGA

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: 852

ATCCGCACCGCTCTTGAAGAGCATTTTGGATCATGTGGAGATATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

ATCCGCACCGCTCTTGAAGAGCATTTTGGATCATGTGGAGATATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

ATCCGCACCGCTCTTGAAGAGCATTTTGGATCATGTGGAGATATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

ATCCGCACCGCTCTTGAAGAGCATTTTGGATCATGTGGAGATATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGGgttagttggc ... tggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgaagtctcccattcttgtcggtgactttacacattgctttgcttggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC
                                      ctttgctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttggctccttgacatatcattcttttatattaggttagagacataattttttcagcaagagattcaggaggaacgttgatattattatgctttcctttggaatgtcatcatctgccgaagtctcccattcttgtcggtgactttacacattgctttgcttggtttgcagAATGGCGTACATGGATTTCAAGGACCCAGATTCCTTGAATAAAGCATACGAGTTGAATGGAACCGACCTTGGTGGCTACAGCTTGTATGTCGATGAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC