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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtcggtttgaattctcgggccggtgcttcgatgactgtttcctcacgcttcgtttgtcggtgtcctcgcag

Basic information

species Zea mays
transcript GRMZM2G110143_T05
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110143_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 5'ss of exon 2
GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtcggtttgaattctcgggccggt-gcttcgatgactgtttcctcacgcttcgtttgtcggtgtcctcgcag-----------
| ||||| ||||||||||| |||||||||||||| |||| ||||||||||||||||||||||||||||||||| || |||| ||| | || |||   |    |||  | | | |  | |   |||||  ||  | |   ||||         | |  |           
GTACCACAGCCGACGACCTCTTCCCGCTCTTCGACCGCTACGGCAAGGTCGTCGACGTCTTCATCCCGAGGGATCGGAGgtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaag
















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|211438564|gb|FL360647.1|FL360647
EST:     CGAGCGCTGCGGGCAAGGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGNACTCGAGGGGGTTTTGCGTTCGTGCGG
genomic: CGAGCGCTGCGG-CAAGG-TCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGG-TTTTGCGTTCGTGCGG
EST: gi|211235451|gb|FL353173.1|FL353173
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|211008119|gb|FL365557.1|FL365557
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|211161811|gb|FL316356.1|FL316356
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTAC
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTAC
EST: gi|149070638|gb|EE159049.2|EE159049
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|78105340|gb|DV523758.1|DV523758
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|149107883|gb|EE292243.2|EE292243
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA

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: 48 (upstream exon), 47 (downstream exon)
Score: 21

GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGT


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 11

GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGT


Block sizes: 32 (upstream exon), 46 (downstream exon)
Score: 14

GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 13

GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGT