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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatcttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA

Basic information

species Zea mays
transcript GRMZM2G030422_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 14
gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatcttattat-attcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
                   |||   |   ||    || ||   | | | | |  || || | |  ||| |  |  |  | | || | ||| || ||| ||  ||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| |
----------------gtgcacctgcagtttttatgctataacgatcaatattaactattggaggctacttttccttacctgttgttatttttcttcgtg--cagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA

upper sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatc-ttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
   ||  || || |   |  ||    || || | |    |  |  |   | |    ||| | | |  |   |   ||   || ||  | |    | |    |||||| || |||||||| ||| | ||||| ||||| || || ||||| ||||||    | ||||||||||||||||| |||||||| ||||||||||||||||
--cttatttaagctgcca--acgaggtagtt-agaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA

upper sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatttgttcagttattatcacagactaattga-tagccattttggtgattttgtaccatcgaaaactaatggttttatcttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
 ||           ||||  ||| |  ||| || ||     | |    | | ||     | |      ||   | | | |||   ||   ||  |     | ||||| || |||||||| ||| | ||||| ||||| || || ||||| ||||||  | | || |||||||||||||||||||||||||| |||||||||||||
ttagccccatgtgaattaaaacaaa--aatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtat---gccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA

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|31356149|gb|CD440506.1|CD440506
EST:     ATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGAT
genomic: ATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAGgtatttgttc ... tcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGAT




















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: 589

GTATGGGAGGCCACTAGTGGAGCTAAGCAATTTACCTTTGAAGGACATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAGgtatttgttc ... tcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

GTATGGGAGGCCACTAGTGGAGCTAAGCAATTTACCTTTGAAGGACATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAGgtatttgttc ... tcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 375

GTATGGGAGGCCACTAGTGGAGCTAAGCAATTTACCTTTGAAGGACATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAGgtatttgttc ... tcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 531

GTATGGGAGGCCACTAGTGGAGCTAAGCAATTTACCTTTGAAGGACATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAGgtatttgttc ... tcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaccatcgaaaactaatggttttatcttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA
              aactaat  putative branch site (score: 531)
                                      ttcttattctt  putative PPT
            aaaactaatggtttta  TA-rich tract