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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagacctcaggatttcaccatttgtaacattttttctgtggaccttgtatttttgctttgttcgtttgcaatccatcctagttatgttatgtttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATGAGAAATACAGACTTCAGAGTCTCAGTAAAGCCTAA

Basic information

species Zea mays
transcript GRMZM2G009030_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------gtaagaagacctcaggatttcaccattt---gtaacattttttctgtggaccttgtatttttgctttgttcgtttgcaatccatccta-gttatgttatgtttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATGAGAAA--TACAGACTTCAGAGTCTCAGTAAAGCCTAA
| | |||| || | ||||| | | |||| ||| | | | | | ||| | | | | |||||| |||| ||||||||||||||||||| ||| |||||| || || ||||||||||| |||||||||||||||||||| | ||||| |||| || || | | | |||| |
gtaaatattcttatcctgttccatatccatttttcaccaacctatactgagattatgtacttccacatgtcatttcctgattctacctcaagtttctccctcgctattttccccattacaccatactatgttttgttcctgtacagCTTCTGCGGATCGAAATGGAGCTAGGCAATGTGCGCTATGCTGGGGAGGCATTCAGGTCTCCCTAAGAAACATACATACCACACAACATTCGGAAAGAGT--
















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|32866424|gb|CF006106.1|CF006106
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGAGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
EST: gi|76290554|gb|DV030122.1|DV030122
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
EST: gi|76011516|gb|DT938686.1|DT938686
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
EST: gi|33102792|gb|CF062752.1|CF062752
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGAGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
EST: gi|149004756|gb|EE039253.2|EE039253
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
EST: gi|76290528|gb|DV030096.1|DV030096
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
EST: gi|7135894|gb|AW498320.1|AW498320
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGAGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA
EST: gi|87156544|gb|DY401333.1|DY401333
EST:     TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGAGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCA

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: 31

ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATGAGAAATACAGACTTCAGAGTCTCAGTAAAGCCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATGAGAAATACAGACTTCAGAGTCTCAGTAAAGCCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27

ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATGAGAAATACAGACTTCAGAGTCTCAGTAAAGCCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaagac ... ttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATGAGAAATACAGACTTCAGAGTCTCAGTAAAGCCTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttgctttgttcgtttgcaatccatcctagttatgttatgtttctgtacagCTTCTGCGGATTGAAGAGGAGCTTGGTAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATGAGAAATACAGACTTCAGAGTCTCAGTAAAGCCTAA
                                          tgtttct  CT-rich tract
 ttatgttat  TA-rich tract