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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgtgagctttcaaagaaacacttcagttagtcttgaaacttcttcattttgatcgcctatctaaccttgtgtggttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG

Basic information

species Zea mays
transcript GRMZM2G028353_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 7
gtaactgtgagctttcaaag-aaacacttcagttagtctt----gaaacttcttcattttgatcgcctatctaaccttgtgtggttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG
|||   |||| |||   ||  ||||| |   | | || ||    |||||  |||  |  | || || ||| ||| | |      ||    | ||||||||| |||||||| |||||||||||||||||||| ||  | |||||||||||||| || |||||||| ||||   ||||||||||||| || |||||
gta--cgtgaacttctgaactaaacattgtgggtggtttttcctgaaacacctttgtagtaatagcatatttaatccttcaatatttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTCGCATCCACACTTCTTGAGAATGG
















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|78109665|gb|DV528081.1|DV528081
EST:     TCAATCCCCTGCATATGCTCTTGGTGAAATTGATGAAGCTGCTCCAG                         GAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGA
genomic: TCAATCCCCTGCATATGCTCTTGGTGAAATTGATGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGA




















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: 102

ACGAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAAAATCAATCCCCTGCATATGCTCTTGGTGAAATTGATGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

ACGAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAAAATCAATCCCCTGCATATGCTCTTGGTGAAATTGATGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

ACGAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAAAATCAATCCCCTGCATATGCTCTTGGTGAAATTGATGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

ACGAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAAAATCAATCCCCTGCATATGCTCTTGGTGAAATTGATGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttgaaacttcttcattttgatcgcctatctaaccttgtgtggttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG
                             atctaac  putative branch site (score: 338)
                                             ttccctgt  putative PPT
             ttcatttt  TA-rich tract