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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatacactttgcataattcaatattgtgtttgagaccctgacgtacgtgtcactttaatagataattttacactgtagaattttgtttcttttgacgtttaccttttcacatatatccattctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCTCATCTTGGGAAATTCTATGGCATTCTGAATGGAATTGATCCAGATATAT

Basic information

species Zea mays
transcript GRMZM2G141399_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141399_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g09230.1 (Oryza sativa), 3'ss of exon 10
gtgagtgatacactttgcataattcaatattgtgtttgagaccctgacgtacgtgtcactttaatagataattttacactgtagaattttgtttcttttgacgtttaccttttcacatatatccattctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCTCATCTTGGGAAATTCTATGGCATTCTGAATGGAATTGATCCAGATATAT
|||||||    | | |    ||   | | || |  |  ||    ||  | |  | |||  ||| ||   ||  | | | | |    |||  | | ||   || | | | | |     | |  |||| | |||||||| ||| | || ||||||||||||||  |||||||||||||||| | |||||||| ||| ||||||||||| ||||| |||||||||||||||||||| |
gtgagtgcctgattgtcttgaag--agttttatcatctag--tttggtgcattt-tcatgtta-tatgaaaaataaaattat----tttcatatgttcaaacatcttcatgtctg--tcttgccataccttgcagGTTTCTCACACGTATTCAAAGGAAGTCGCAGGTCATGGTGCCATAGCTCCTCATCGTGGAAAATTCTATGGAATTCTCAATGGAATTGATCCAGATATCT
















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|31352858|gb|CD437215.1|CD437215
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|33091960|gb|CF051954.1|CF051954
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCAACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATAGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|31361027|gb|CD445384.1|CD445384
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|31357767|gb|CD442124.1|CD442124
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|67022688|gb|CO451437.1|CO451437
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|67014870|gb|CO443619.1|CO443619
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|37419287|gb|CF647322.1|CF647322
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|32933471|gb|CF038283.1|CF038283
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCAACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATAGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
EST: gi|24769423|gb|CA404552.1|CA404552
EST:     GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACT                         GTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT
genomic: GAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCT

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 78

TAGCTTGGCAAATGCACGGGTGGTATTCACCATCCACAATCTTGAATTTGGAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCTCATCTTGGGAAATTCTATGGCATTCTGAATGGAATTGATCCAGATATAT


Block sizes: 40 (upstream exon), 31 (downstream exon)
Score: 11

TAGCTTGGCAAATGCACGGGTGGTATTCACCATCCACAATCTTGAATTTGGAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCTCATCTTGGGAAATTCTATGGCATTCTGAATGGAATTGATCCAGATATAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

TAGCTTGGCAAATGCACGGGTGGTATTCACCATCCACAATCTTGAATTTGGAGCGCATCATATTGGCAAAGCAATGAGATATTGTGATAAAGCCACAACTgtgagtgata ... ttctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCTCATCTTGGGAAATTCTATGGCATTCTGAATGGAATTGATCCAGATATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagaattttgtttcttttgacgtttaccttttcacatatatccattctttgcagGTCTCTAATACATATTCAAAGGAAGTGTCAGGTCATGGTGCCATCGTTCCTCATCTTGGGAAATTCTATGGCATTCTGAATGGAATTGATCCAGATATAT
               ttttgac  putative branch site (score: 112)
                                         tccattcttt  putative PPT
     attttgtttctttt  TA-rich tract