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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG

Basic information

species Zea mays
transcript GRMZM2G112865_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 2
gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
                    |||      | | | |  ||  ||  ||  || ||      ||  ||    |||      ||   |||||    |   |  |  ||       | |||| ||  || |||||||||||||| ||||| ||||||||||||||||||||||| ||||| |||
--------------------gtacgt-actctctcctttccgcctaggatctggt------cgaacac--cttg-----tagagtgggggcgcctcggatttatgtgctgggagtcgtggttgattccagGCGAAGGAGGTGCGGCGCAAGGCGGATCAGATGGTGCAGCTCGGGAAAGAG

upper sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 2
---gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttc-----gtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
   |      | || ||||||     | ||||  |||  | |||| ||     || | ||||||   ||||| |||  || ||||||      | ||| ||   |   ||| || ||   ||||||     |||||||||||||||||| |||  ||| |||||||||||||||||||| || || |||
gtagcccgcgtcctgtctctccgtggttccggcattt--cgtcgaacac----ctagcggtgggaatgcaggttttctgcgccaggaaatt--tgatttttttttttcttttctgtgtgttgcttcttgacgtttcagGCGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAG
















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|32909297|gb|CF014109.1|CF014109
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTCGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|50337604|gb|CO532730.1|CO532730
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|110963515|gb|EE183415.1|EE183415
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|37393499|gb|CF634015.1|CF634015
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|211500584|gb|FL212575.1|FL212575
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|60356193|gb|DN223166.1|DN223166
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|50337603|gb|CO532729.1|CO532729
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|148963908|gb|EE015020.2|EE015020
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG

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: 215

GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 221

GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 228

GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 343

GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
                   tgttaac  putative branch site (score: 343)
                                            cttcgtttc  putative PPT
               taattgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG