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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccgtaattgccatctttccatgatctggggttgtttcttactcaacgcagatccgtgacacccttgccgctttgtttatttgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG

Basic information

species Zea mays
transcript GRMZM5G841619_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841619_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g08430.1 (Oryza sativa), 3'ss of exon 7
gtaaaccgtaattgccatctttccatgatctggggttgtttcttactcaacgcagatc--cgtgacacccttgccgctttgtttatttgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG
||||| | || |    | |||    | |     |  |   | | | ||  | ||  ||   |    ||| ||| |||||  ||   |||  |  |||||||| ||||||||||||||||||||||| || || |||||  || ||| |   ||||  ||||||||||| || |||||||||||||||||||||||||
gtaaatcatactcaagaacttatgttcaaaacagtatacgtttaattccccccaattcattgcatgacctttgtcgcttcattc-cttgtaa--cagATTGCGGGATGGGGCGCAGATGGTGTGATCATTGGGAGCGCTATGGTGAGGCAATTGGGCGAAGCTGCTTCACCCGAAGAAGGATTGAAGAAGCTAGAAG
















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|166492891|gb|EG101886.1|EG101886
EST:     GTGTGTCGACTCCAGAGCATGTCCGGCAG                         ATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
genomic: GTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
EST: gi|211089057|gb|FL454767.1|FL454767
EST:     AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG                         ATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
genomic: AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
EST: gi|7118996|gb|AW497556.1|AW497556
EST:     AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG                         ATTGCAGGATTGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
genomic: AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
EST: gi|78025299|gb|DV493686.1|DV493686
EST:     AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG                         ATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
genomic: AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
EST: gi|6827013|gb|AW330656.1|AW330656
EST:     AACCCGNGGCTGNTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG                         ATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
genomic: AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
EST: gi|4874356|gb|AI673876.1|AI673876
EST:     AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG                         ATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
genomic: AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAG
EST: gi|32863333|gb|CF003015.1|CF003015
EST:     AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG                         ATTGCAGGATGGGGC
genomic: AACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGC

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: 46 (upstream exon), 48 (downstream exon)
Score: 63

GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 525

GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 974

GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAGgtaaaccgta ... tgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttactcaacgcagatccgtgacacccttgccgctttgtttatttgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG
 ttcttac  putative branch site (score: 225)
                                       tttattt  putative PPT
                                   tttgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccgtaattgccatctttccatgatctggggttgtttcttactcaacgcagatccgtgacacccttgccgctttgtttatttgctattcagATTGCAGGATGGGGCGCAGATGGTGTGATTATCGGTAGCGCAGTGATGAAGACGTTGGAGGAAGCTGCTTCTCCAGAAGAAGGATTGAAGAAGCTAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC