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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatttcatgcttcacaattagattggttttttaaggttctcatttgtctcttacttactaatggctacttttaccttctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTATATCATTTTACAAAAGATACTCAAAACCAAACG

Basic information

species Zea mays
transcript GRMZM2G018508_T01
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 28
gtatgttattt------catgcttcacaa---ttagattggttttttaaggttctcattt------gtctcttacttactaatggctacttttaccttctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTATATCATTTTACAAAAGATACTCAAAACCAAACG
|||| |||  |      |  | || ||||     |  ||  ||| |||||    ||| |         | |  |   | | |||| | |  || | || |||||||||||||| || || || ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||| |||||||| || |||
gtatattacctttgtgtccggttttacaagatcaattttcatttgttaagaggttcaatccctcaatccccccaggaattgatggatgccattcctttttctttctagGTTCCGGAGGAAGAGAAAAATCTTGGTCCTTTTGATCGCTTGATTCATGTATACCATTTTACCAAAGACACTCAAAATCAGACG
















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|6020900|gb|AW065828.1|AW065828
EST:     AAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAG                         GTTCCAGATGAGGAGAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTA
genomic: AAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAGgtatgttatt ... ctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTA
EST: gi|67015347|gb|CO444096.1|CO444096
EST:     AAAAGATTGAAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAG                         GTTCCAGATGAGGAGAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTA
genomic: AAAAGATTGAAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAGgtatgttatt ... ctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 194

GTGTTTGCACCAAATGAAAAGATTGAAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAGgtatgttatt ... ctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTATATCATTTTACAAAAGATACTCAAAACCAAACG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 73

GTGTTTGCACCAAATGAAAAGATTGAAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAGgtatgttatt ... ctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTATATCATTTTACAAAAGATACTCAAAACCAAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

GTGTTTGCACCAAATGAAAAGATTGAAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAGgtatgttatt ... ctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTATATCATTTTACAAAAGATACTCAAAACCAAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 132

GTGTTTGCACCAAATGAAAAGATTGAAAACATTAATGATCAGTACTGGACACTGCGTGCGGAGGAGgtatgttatt ... ctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTATATCATTTTACAAAAGATACTCAAAACCAAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggttctcatttgtctcttacttactaatggctacttttaccttctctttctagGTTCCAGATGAGGAAAAAAACCTTGGTCCCTTTGATCGATTGATTCATGTATATCATTTTACAAAAGATACTCAAAACCAAACG
                       tactaat  putative branch site (score: 132)
                                ctacttttaccttctc  putative PPT
                      ttactaat  TA-rich tract