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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatattctgtgtgatcaaatcattttccttctcaatttttaagagcaattatatttagaattacttttccacatataaaatatcactgtactgacacactcaatatatgttttatctttgaaatgttgatcaggaaatgtaacccaatttgaattttctatcgactttttttaatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG

Basic information

species Zea mays
transcript GRMZM2G381395_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381395_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os09g07120.1 (Oryza sativa), 3'ss of exon 9
gtattgatattctgtgtgatcaaatcattttccttctcaatttttaagagcaattatatttagaattacttttccacatataaaatatcactgtactgac-acactcaatatatgttttatctttga-aatgttgatcaggaaatgtaacccaatttgaattttctatcgactttttttaatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG
                                                                                |||    ||    | | | | || | ||| | |  ||| || || |  ||  || |     |  | ||| |  |  |  | |  |     | |||  ||    ||| ||||||| ||||||||||| ||||| |||||||| || ||||||| |||||||
--------------------------------------------------------------------------------taatccttctaaatgcagtctactcgcaacacagttttgattttcgctaagattcacttccatgtttaatcataactacaataac-----attttcctt----tttcagGATGGTTCTTGTAATGGCCTGCAGCACTATGCTGCTCTTGGAAGGGATAAG
















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|32931335|gb|CF036147.1|CF036147
EST:     TAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAG                         GATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGG
genomic: TAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAGgtattgatat ... aatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGG
EST: gi|74240732|gb|DT648646.1|DT648646
EST:     TAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAG                         GATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG
genomic: TAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAGgtattgatat ... aatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG

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: 124

TGAAGATCCATTCCAGTGCCTGGCAGTATGCATGAATCTCACTGAAGCTTTAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAGgtattgatat ... aatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

TGAAGATCCATTCCAGTGCCTGGCAGTATGCATGAATCTCACTGAAGCTTTAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAGgtattgatat ... aatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 68

TGAAGATCCATTCCAGTGCCTGGCAGTATGCATGAATCTCACTGAAGCTTTAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAGgtattgatat ... aatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

TGAAGATCCATTCCAGTGCCTGGCAGTATGCATGAATCTCACTGAAGCTTTAAGAAGCTCGTCTCCAGAAACAACAATCTCACATATTCCTGTGCACCAGgtattgatat ... aatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcaggaaatgtaacccaatttgaattttctatcgactttttttaatattttagGATGGCTCTTGTAATGGTCTGCAACACTATGCGGCACTTGGAAAGGATAAG
                                         ttttaat  putative branch site (score: 72)
                                     cttttttta  CT-rich tract
                  aatttgaattttctat  TA-rich tract