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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggacacttgttttagctatttatcccttttccatttatatcttttgttctgtgcaaaaattaattccaagtaaatcatattgtaatccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG

Basic information

species Zea mays
transcript GRMZM2G130351_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130351_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 7
gtatggacac----ttgttttagctattta-tcccttttccatttatatcttttgttctgtgcaaaaattaattccaagtaaatcatattgtaatccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG
||||   ||     || ||||| || || | | || | |||| |   |     |  |  |||  |  |   | || || |||| | | ||   |||||  |||||| ||||||||| ||||||| |||||||||||||||||||| ||||||||||||||||| ||||||||||| ||||||| ||||
gtatttgcatcagtttattttacctcttcaattccatatccagtagaaaaaaattgttcgtgtgattacccagtctaaataaaccttgttcgtatccatgtaagGTGCCTTTTGAAGAAGTTCCAGATCTTGTTGCCAGCCGCCGAGTATTTCTTTCAAAAGGATATGCTTATGTTGCGATGAGTCAG
















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|78118655|gb|DV537039.1|DV537039
EST:     AAATGTTGATCATGTGTTCTTCAAG                         GTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTT
genomic: AAATGTTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTT
EST: gi|149081470|gb|EE170604.2|EE170604
EST:     AAATGTTGATCATGTGTTCTTCAAG                         GTACCTTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCT
genomic: AAATGTTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTT-GAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCT
EST: gi|148953215|gb|EE152697.2|EE152697
EST:     AAATGTTGATCATGTGTTCTTCAAG                         GTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTT
genomic: AAATGTTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTT
EST: gi|76021633|gb|DT948803.1|DT948803
EST:     AAATGTTGATCATGTGTTCTTCAAG                         GTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTT
genomic: AAATGTTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTT

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: 20 (upstream exon), 43 (downstream exon)
Score: 78

TTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG


Block sizes: 20 (upstream exon), 43 (downstream exon)
Score: 8

TTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG


Block sizes: 20 (upstream exon), 42 (downstream exon)
Score: 11

TTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG


Block sizes: 19 (upstream exon), 31 (downstream exon)
Score: 1

TTGATCATGTGTTCTTCAAGgtatggacac ... tccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgttctgtgcaaaaattaattccaagtaaatcatattgtaatccaattaagGTACCTTTTGAACAAGTTCCTGATCTTGTTGCCAGCCGCCGGGTATTTCTTTCAAAAGGCTATGCTTATGTGGCGATGAATCAG
                 aattaat  putative branch site (score: 1)
              aaaaattaattccaag  TA-rich tract