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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtactgggcaaattccatcttttggtctaacacatgaattacaatggcggctgatctttctttcttactggacttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGCTGGGCCACTGCTGTCGAAGCTTTAAG

Basic information

species Zea mays
transcript GRMZM2G154574_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154574_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g33100.1 (Oryza sativa), 3'ss of exon 8
gtatgtactggg--caaattccatcttttggtctaacacatgaattacaatggcggctgatctttctttcttactggacttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGCTGGGCCACTGCTGTCGAAGCTTTAAG
|||  || |||   |||| |  |  | ||| |||| |   || | ||  |||||  || | | ||  | |||  |  |||   ||||| |  ||||||| || || |||||||| ||||| ||||| |||||||||||||||| |||||||||    ||||||||
gta-atattggttccaaagtttacttgttgatctacc---tgcactaggatggcttctaaccatt--tacttctttaactgatattagGGGATTGCTGACCGTGTTTGTCTTGGGTTGTTGCCCTCGAGTGAATGTAGCTGGGACACTGCTGTGAGGGCTTTAAG
















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|87155467|gb|DY400256.1|DY400256
EST:     AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         GGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
genomic: AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
EST: gi|113679358|gb|DW836903.1|DW836903
EST:     ATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         AGTGTTGCTGATCGAGTCTGTCTTGGAATTGTTACCCTCAAGTGAA
genomic: ATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGA-TTGTTACCCTCAAGTGAA
EST: gi|26559427|gb|CA831662.1|CA831662
EST:     AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         GGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
genomic: AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
EST: gi|26559057|gb|CA831292.1|CA831292
EST:     AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         GGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
genomic: AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
EST: gi|22542262|gb|BU092700.1|BU092700
EST:     AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         GGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
genomic: AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
EST: gi|32942516|gb|CF047335.1|CF047335
EST:     AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         GGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
genomic: AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
EST: gi|87155759|gb|DY400548.1|DY400548
EST:     AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         GGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
genomic: AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
EST: gi|22935761|gb|BU572036.1|BU572036
EST:     AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAA                         GGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC
genomic: AGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGC

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), 48 (downstream exon)
Score: 31

TCCACATGCTCTGGAGGCTCTTCGGCGCAATGTTAGTGACAACAGAGTGGAGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGCTGGGCCACTGCTGTCGAAGCTTTAAG


Block sizes: 27 (upstream exon), 37 (downstream exon)
Score: 2

TCCACATGCTCTGGAGGCTCTTCGGCGCAATGTTAGTGACAACAGAGTGGAGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGCTGGGCCACTGCTGTCGAAGCTTTAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 19

TCCACATGCTCTGGAGGCTCTTCGGCGCAATGTTAGTGACAACAGAGTGGAGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGCTGGGCCACTGCTGTCGAAGCTTTAAG


Block sizes: 35 (upstream exon), 41 (downstream exon)
Score: 15

TCCACATGCTCTGGAGGCTCTTCGGCGCAATGTTAGTGACAACAGAGTGGAGGATCGATGTATTATACTTGAAGGAGATAACCGGGTGACTGCACCCAAAgtatgtactg ... cttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGCTGGGCCACTGCTGTCGAAGCTTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacacatgaattacaatggcggctgatctttctttcttactggacttgaattagAGTGTTGCTGATCGAGTCTGTCTTGGATTGTTACCCTCAAGTGAATGTAGCTGGGCCACTGCTGTCGAAGCTTTAAG
                                  ttcttac  putative branch site (score: 15)
         aattacaat  TA-rich tract