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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgttgttgccattttgtttgtttgtttgtttgtttctttcttttccggtcgttcaacccgtacgtactgtgcatatatatttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTGCTCATTGCCGG

Basic information

species Zea mays
transcript GRMZM2G041980_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041980_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g13870.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------gtaagtc-gttgtt--gccattttgtttgtttg--tttgtttgtttctttcttttccggtcgttc--aacccgta--cgtactgtgcatatatat--ttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTGCTCATTGCCGG
                                                                                 ||  || ||  ||       |    |  || |  |   |||| | ||   |  || |   |||   ||    ||    |  ||  |||||  ||   ||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| ||||| ||
gtaagctacctagcacgattttaattcatttaatttaattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTGCTGATTGCTGG
















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|211214509|gb|FL039232.1|FL039232
EST:     CATTCTACCTCATGTTCGTCATCTCCGGCGTCGC-ACGGACAACAGAGCA                         ATCGGGGGAGCTGGCTG
genomic: CATTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACGGACAACAGAGCAgtaagtcgtt ... atatttgcagATCGGGG-AGCTGGCTG
EST: gi|86473885|gb|DY240255.1|DY240255
EST:     CGGACAACAGAGCA                         ATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTG
genomic: CGGACAACAGAGCAgtaagtcgtt ... atatttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTG

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: 89

GCTGCCCACGGGCTCCGAGGTGCAGTCGCTCGTCATCGAGATCATCACCACATTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACGGACAACAGAGCAgtaagtcgtt ... atatttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTGCTCATTGCCGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 42

GCTGCCCACGGGCTCCGAGGTGCAGTCGCTCGTCATCGAGATCATCACCACATTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACGGACAACAGAGCAgtaagtcgtt ... atatttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTGCTCATTGCCGG


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 4

GCTGCCCACGGGCTCCGAGGTGCAGTCGCTCGTCATCGAGATCATCACCACATTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACGGACAACAGAGCAgtaagtcgtt ... atatttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTGCTCATTGCCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GCTGCCCACGGGCTCCGAGGTGCAGTCGCTCGTCATCGAGATCATCACCACATTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACGGACAACAGAGCAgtaagtcgtt ... atatttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTGCTCATTGCCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctttcttttccggtcgttcaacccgtacgtactgtgcatatatatttgcagATCGGGGAGCTGGCTGGGCTGGCCGTGGGCGCAACCATCCTGCTTAACGTGCTCATTGCCGG
                                         atatatattt  TA-rich tract