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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacaaacatcaaataatatctatcggagatagagcttgtgaagttttcttttcctaacttctttgctgtgcttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG

Basic information

species Zea mays
transcript GRMZM2G160569_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g44070.1 (Oryza sativa), 3'ss of exon 8
gtaatacaaacatcaaataatatctatcggagatagagcttgtgaagttttcttttcctaacttctttgctg-tgcttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG
||||   |||||||||  | |||||| |  ||||| |    || |  |||||      |   ||  |   || ||||  ||||||||||||||||||||||||||| |||||| ||| | ||| ||||||||| ||||||||||||| ||||| |||||||||
gtaaggaaaacatcaagaagtatctaacaaagatatacacagttagtttttcacaatttctttttctaattggtgctctctacagTGCTTTTTCCCCCAGAATGTGGTGCCAAACATTCAAACTCCAACTTTTATTTTGAACACTGCTTATGATGTGTGGCAG
















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|211266712|gb|FL294975.1|FL294975
EST:     CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG                         TGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT
genomic: CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT
EST: gi|67018103|gb|CO446852.1|CO446852
EST:     CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG                         TGCTTTTTCCCCCAGAATGTGTTGCCAACCATTCGAACTCCAACTTTTGTT
genomic: CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT
EST: gi|31356908|gb|CD441265.1|CD441265
EST:     CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG                         TGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT
genomic: CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT
EST: gi|31356050|gb|CD440407.1|CD440407
EST:     CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG                         TGCTTTTTCCCCCAGAATGTGTTGCCCACCATCCGAACCCCA-CTTTTGTT
genomic: CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT
EST: gi|32837541|gb|CD977219.1|CD977219
EST:     CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG                         TGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT
genomic: CTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTT

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: 198

GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 367

GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 416

GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCGgtaatacaaa ... cttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatagagcttgtgaagttttcttttcctaacttctttgctgtgcttcctacagTGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG
                          tcctaac  putative branch site (score: 416)
                                           tgcttcct  putative PPT
                  ttttctttt  TA-rich tract