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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcattaaaatttttactacctacattgttcatgtgttttcttggcttactccaccactaagtatttttaatgtacacttgtgacag

Basic information

species Zea mays
transcript GRMZM2G458538_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458538_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 5'ss of exon 12
TGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcattaaaatttttactacctacattgttcatgtgttttcttggcttactccaccactaagtatttttaatgtacacttgtgacag
||||||||||||||| ||||| ||||||||||||||||||| |||||| || ||||||||||||||||||   ||   | || |      ||  ||| | |  ||| |||||||  |     ||||||   ||||||  |    ||   | ||
TGTTTATATCTGCCTACGCAACTGCACCCAGCAGTTGAGGAGTGCCTCCTTGGCTCTTTTCGCgtaagcacctaa---tataatg-----atgtttctttttctttattggctttattttttactaaga--ttttaacctgttttttcaatag
















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|60338618|gb|DN205591.1|DN205591
EST:     CTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC                         ATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTG
genomic: CTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcatta ... cttgtgacagATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTG
EST: gi|86465843|gb|DY232216.1|DY232216
EST:     CTGCGCAATTGCCCCCAGCAGTTGAGGAATGCCTCTTTATCTCTTTTCGC                         GTGGTTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTG
genomic: CTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcatta ... cttgtgacagATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTG

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), 47 (downstream exon)
Score: 84

TGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcatta ... cttgtgacagATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTGGCTTAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 97

TGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcatta ... cttgtgacagATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTGGCTTAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 119

TGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcatta ... cttgtgacagATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTGGCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

TGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGCgtaagcatta ... cttgtgacagATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTGGCTTAG