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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCGATGCCCGCCGCCTGAGAGAGGCCCGCACCACCACCGTCGCCCTCGGCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgccatctttcctccgccgctttgcccgtcttgcttgtctcgcgttcttcaactgttcgacgaattgtctttgcag

Basic information

species Zea mays
transcript GRMZM2G123305_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123305_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g20689.1 (Oryza sativa), 5'ss of exon 1
CATCGATGCCCGCCGCCTGAGAGAGGCCCGCACCACCACCGTCGCCCTCGGCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatac----------gccatctttcctccgccgctttgcccg----tcttgcttgtctcg-----cgttcttcaactgttcgacgaattgtcttt-gcag-------------
|  ||| || |||||||     ||||||||| | |||||||||||||||| ||||||||||||||| || || ||||| ||||||||| | ||||||||||||  ||          |||    | |  ||  | || | ||||    |||| ||  | | |     ||| |  || || || |||||| || ||   | |              
CCCCGACGCGCGCCGCCCCGCCGAGGCCCGCCCAACCACCGTCGCCCTCGCCGCCGTGTCCTCCGCCCACGGCTCCGCCCTCGTCCGCCTCGGCGACACCgtacgaccccccaagccgccgctctccacccctccctctccccgccactcttcctgatttaggcgtccgtgcaccacctatttgacgaaatgcctcccgtatctgtttgcggcag
















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|78109449|gb|DV527865.1|DV527865
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
EST: gi|31359716|gb|CD444073.1|CD444073
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
EST: gi|37424194|gb|CF649828.1|CF649828
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGC
EST: gi|60400680|gb|DN233487.1|DN233487
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
EST: gi|67041329|gb|CO467584.1|CO467584
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCTTTCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
EST: gi|40334570|gb|CK368640.1|CK368640
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
EST: gi|76293265|gb|DV032833.1|DV032833
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
EST: gi|211040937|gb|FK998650.1|FK998650
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
EST: gi|211189642|gb|FL055471.1|FL055471
EST:     GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACC                         GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC
genomic: GCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTAC

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: 40 (upstream exon), 48 (downstream exon)
Score: 12

CATCGATGCCCGCCGCCTGAGAGAGGCCCGCACCACCACCGTCGCCCTCGGCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 25

CATCGATGCCCGCCGCCTGAGAGAGGCCCGCACCACCACCGTCGCCCTCGGCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 10

CATCGATGCCCGCCGCCTGAGAGAGGCCCGCACCACCACCGTCGCCCTCGGCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT


Block sizes: 29 (upstream exon), 48 (downstream exon)
Score: 8

CATCGATGCCCGCCGCCTGAGAGAGGCCCGCACCACCACCGTCGCCCTCGGCGCCGTGTCCTCCGCGCATGGTTCCGCTCTCGTCCGCGTTGGCGACACCgtaatacgcc ... gtctttgcagGCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT