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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattttgatggccagaatgttaggcatcattttcatattagatgataacagcctgataatgtattgaccttttgttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA

Basic information

species Zea mays
transcript GRMZM2G015132_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 11
gtaaattttgatggc-cagaatgttaggcatcattttcatattagatgataacagcctgataatgtattgaccttttgttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA
||||||||  |||   |||||| || |  |   |  |  ||   |||| ||   | |||||| |||||| | ||| | || |   |||||||||||||| ||| |||||   || ||||| || ||||||||||| ||||||||||| || || |||||||| || ||| || |
gtaaatttcaatgatacagaatctt-gttaggttgattttagccgatgctattggtctgatagtgtatt-atcttctattcttcacagGTTACTGCAAACCGCCTGCTAAGCTCTAAACAAACTATTCCTCATTATTACTTGACAGTTGACGCCCGTGTTGATAATCTTATCAA

upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G03930.2 (Glycine max), 3'ss of exon 11
----------gtaaattttgatggccagaatgttaggcatcattttcatattagatgataacagcc--tgataatgtattgaccttttgttgtctt-cagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA
          || |  |||      || ||   ||   ||  || || | |   |  || | ||    |  | |   |   ||  |   |  | || ||||| || ||    ||  | |||  ||| ||||| || |||||||||||||| || ||||||||| || |||||||||||||      
gtaagaatgagtgatgtttttgaaacaaaactatacatatttttatcttgtgtaagcatgagagatgttttttaaacaaaaactatacatatttttacagGTCACAGCTTCACGGCTACTATTATCAAAACAAACTATTCCTCATTACTATTTAACAGTAGATACATGTGTTGACAAACTCACGAG

upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 12
-------------------------------------------------------------------------------------------------gtaaattttgatggccag----aatgttaggcatcattttcatattagatgataacagcctgataatgta---ttgaccttttg---ttgtctt--cagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA
                                                                                                 | ||  ||| |   | |     ||| ||    ||  ||   || ||||   ||   ||| | ||  | |    |  || |||||   ||  |||  ||| | || ||    ||| |  ||  |||||| ||||| ||||| ||||| || |||||||| ||| || |||||||||||||| |  |
gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatat-ttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA

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|32789248|gb|CD941484.1|CD941484
EST:     GATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG                         GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
genomic: GATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
EST: gi|74235054|gb|DT642968.1|DT642968
EST:     CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG                         GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
genomic: CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
EST: gi|32840355|gb|CD980036.1|CD980036
EST:     CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG                         GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
genomic: CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
EST: gi|32938642|gb|CF043461.1|CF043461
EST:     CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG                         GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
genomic: CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
EST: gi|32932311|gb|CF037123.1|CF037123
EST:     CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG                         GTCACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC
genomic: CAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTAC

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: 165

CTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

CTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

CTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 297

CTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAGgtaaattttg ... ttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcatattagatgataacagcctgataatgtattgaccttttgttgtcttcagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA
                                tattgac  putative branch site (score: 297)
                                      ccttttgttgtcttc  CT-rich tract
     atattagatgataa  TA-rich tract