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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaccatcgatgccgccgctgcactgcagctcctgctgcaaatgccgacgctccttacaacgtaatataatggctgcttttgcttgtccggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCGCACATCCTCGTCTTCAGCGAGGACCTCTTCTTCATCTACCTCCTACCTC

Basic information

species Zea mays
transcript GRMZM2G027851_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 1
gtaagcaccatcgatgccgccgctgcactgcagctcctgctgcaaatgccgacgctccttaca-acgtaatataatggctgcttttgcttgtccggccgg-cagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCGCACATCCTCGTCTTCAGCGAGGACCTCTTCTTCATCTACCTCCTACCTC
|||||| | |   |  ||   ||||   |  |      | |  |   |||   | | || ||  |||     |  | | || ||| |||||   |   || |||||||| ||||||||||| |||||| ||||||  ||||| ||||||||||||||| |  |||||||||| ||||| |||||||||||||||||||| ||||
gtaagcgc-acacacaccattgctgtgattgattgatcgattgattcgccattgttgctgacgcacgcttgctgctcgatgattt-gcttgcttgcttgggcagGGGCTCTGCACCGGCGTGGTGATCTTGCTGATGACCAAAGGGAAGAGCTCGCACTTATTCGTCTTCAGTGAGGATCTCTTCTTCATCTACCTCCTCCCTC
















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|74239375|gb|DT647289.1|DT647289
EST:     TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATC                         GGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
genomic: TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
EST: gi|50333105|gb|CO528231.1|CO528231
EST:     TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATC                         GGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
genomic: TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
EST: gi|93282181|gb|EB674445.1|EB674445
EST:     TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATC                         GGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
genomic: TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
EST: gi|78093453|gb|DV521827.1|DV521827
EST:     TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATC                         GGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
genomic: TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
EST: gi|78115473|gb|DV533861.1|DV533861
EST:     TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATC                         GGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG
genomic: TCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCG

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), 47 (downstream exon)
Score: 69

CATCAACCTGTTCGTCGCGCTGCTCTGCGCCTGCATCGTCCTGGGCCACCTCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCGCACATCCTCGTCTTCAGCGAGGACCTCTTCTTCATCTACCTCCTACCTC


Block sizes: 37 (upstream exon), 41 (downstream exon)
Score: 36

CATCAACCTGTTCGTCGCGCTGCTCTGCGCCTGCATCGTCCTGGGCCACCTCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCGCACATCCTCGTCTTCAGCGAGGACCTCTTCTTCATCTACCTCCTACCTC


Block sizes: 43 (upstream exon), 38 (downstream exon)
Score: 11

CATCAACCTGTTCGTCGCGCTGCTCTGCGCCTGCATCGTCCTGGGCCACCTCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCGCACATCCTCGTCTTCAGCGAGGACCTCTTCTTCATCTACCTCCTACCTC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 36

CATCAACCTGTTCGTCGCGCTGCTCTGCGCCTGCATCGTCCTGGGCCACCTCCTGGAGGAGAACCGCTGGGTTAACGAGTCCATCACCGCGCTCATCATCgtaagcacca ... cggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCGCACATCCTCGTCTTCAGCGAGGACCTCTTCTTCATCTACCTCCTACCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgacgctccttacaacgtaatataatggctgcttttgcttgtccggccggcagGGGCTGTGCACCGGCGTCGTGATCCTGCTGACCACCAAGGGGAAGAGCTCGCACATCCTCGTCTTCAGCGAGGACCTCTTCTTCATCTACCTCCTACCTC
        tccttac  putative branch site (score: 36)
                                       cttgtcc  putative PPT
                   taatataat  TA-rich tract