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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctcacaaatccaattccttttgctcatattgttaatgcgtttcagtacttgattagcagatattctagcatttggcgcatcaactcattgactgctgcaatgctgtgctgttgtctattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTCATTCAGATAAACAGCGAGGTTGCCATGGGGGCTAGTATCTTCCCCATCT

Basic information

species Zea mays
transcript GRMZM2G125516_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125516_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g10530.1 (Oryza sativa), 3'ss of exon 5
gtaagtctcacaaatccaat--tccttttgctcatattgttaatg------cgtt---------------tcagtacttgattagcagatattctagcatttggcgcatcaact-cattgactgctgcaat-gct---gtgctgttgtctattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTCATTCAGATAAACAGCGAGGTTGCCATGGGGGCTAGTATCTTCCCCATCT
|||||| |||||||  |||   ||| | |||| ||| | || |||       |||               || |||||     | |||| |||||    || |  |||| |||| |  || |   | |  | |||   |   ||  |||| ||||| |||||||||| |||||||| ||||| ||||||||||| |||||||| || ||||||||||| ||||||||| | |||||||| || || |||||||||||||
gtaagtttcacaaactcaacaatccatatgcttatactattgatggtacattgttatactattaatgttctctgtactctggcaacagacattctgttgtt-gatgcattaacttcggtgtcccttacgtttgctttcgcattggggtcttttttgtagAGTGATGCTTACCAAGCAACAGGGTGCTACAACATATTGTGCTCCGGATTCATTCAGATCAACAGCGAGATCGCCATGGGCGCGAGCATCTTCCCCATCT
















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|24773757|gb|CA409011.1|CA409011
EST:     GCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACT                         AGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTC
genomic: GCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACTgtaagtctca ... tattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTC
EST: gi|149083882|gb|EE173258.2|EE173258
EST:     GCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACT                         AGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTC
genomic: GCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACTgtaagtctca ... tattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTC
EST: gi|30306496|gb|CD001169.1|CD001169
EST:     GCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACT                         AGTGATGCATACCAAGCCCACAGGTTGCTACAACATGTTGTGCTCTGGTTT
genomic: GCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACTgtaagtctca ... tattttgcagAGTGATGCATACCAAGCC-ACAGGTTGCTACAACATGTTGTGCTCTGGTTT

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: 333

GTTAGCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACTgtaagtctca ... tattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTCATTCAGATAAACAGCGAGGTTGCCATGGGGGCTAGTATCTTCCCCATCT


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 34

GTTAGCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACTgtaagtctca ... tattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTCATTCAGATAAACAGCGAGGTTGCCATGGGGGCTAGTATCTTCCCCATCT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 35

GTTAGCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACTgtaagtctca ... tattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTCATTCAGATAAACAGCGAGGTTGCCATGGGGGCTAGTATCTTCCCCATCT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 51

GTTAGCCCTGACCTCTATGGAGACAACAACACCAGGCTGTTCACATATTGGACTgtaagtctca ... tattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTCATTCAGATAAACAGCGAGGTTGCCATGGGGGCTAGTATCTTCCCCATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggcgcatcaactcattgactgctgcaatgctgtgctgttgtctattttgcagAGTGATGCATACCAAGCCACAGGTTGCTACAACATGTTGTGCTCTGGTTTCATTCAGATAAACAGCGAGGTTGCCATGGGGGCTAGTATCTTCCCCATCT
               cattgac  putative branch site (score: 51)
                                           tctatttt  putative PPT
                                           tctatttt  TA-rich tract