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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcgataaaacattaaaacattgctctttctaaattctaatcatgcgctcgatcataaccgacgtgtatggttcacggccatgtgcatcttgtaatgcagaggccagggcgatctatgaccccgttgttgtctaaaaaaaatgcgtgctattttgctccttgatatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG

Basic information

species Zea mays
transcript GRMZM2G124918_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 7
gtatgtcgataaaacattaaaacattgctctttctaaattctaatcatgcgctcgatcataa--ccgacgtgtatggttcacggccatgtgcatcttgtaatgcagaggccagggcgatctatgaccccgttgttgtctaaaaaaaatgcgtgctattttgctccttgata--tgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG
                                               || ||  ||| | |   ||    | | ||    |      |||| | ||   | |  | |      || | | || |  | |     | | |||  | ||    |     ||| ||||||| |   | |||||||||| || || |||||||| ||  |||| || ||||||||||||||||| || |||||||| || |||||||| ||||| ||||||||||||||
----------------------------------------------gtgtgca-gataaaagtccctttttttctgaaatatcattttgtgaaact-acactatacaatttgaggtgttgtacgcactcaactgtatataattagaacttatttatatttactccttgtttcttaatgcagGTCCCAAGATCTGGTTTCTTGCTGTCATCTATTTCATTCTTGGATGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAG
















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|95107983|gb|EB740212.1|EB740212
EST:     CCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAG                         GTCCTAAGATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCAG
genomic: CCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAGgtatgtcgat ... tatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCG
EST: gi|71766083|gb|DR964020.1|DR964020
EST:     CCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAG                         GTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCG
genomic: CCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAGgtatgtcgat ... tatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCG
EST: gi|78111675|gb|DV530072.1|DV530072
EST:     CCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAG                         GTCCCTAAA-TATGGTTTCTCGCAATC
genomic: CCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAGgtatgtcgat ... tatgatgcagGTCC-TAAAATATGGTTTCTCGCAATC

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

GGTTGGTCGTGTGCCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAGgtatgtcgat ... tatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

GGTTGGTCGTGTGCCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAGgtatgtcgat ... tatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

GGTTGGTCGTGTGCCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAGgtatgtcgat ... tatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GGTTGGTCGTGTGCCTGTTTTGGAACATAATCTGCGTTACGGCTGCCTGGGCAAAAGGGTCAGgtatgtcgat ... tatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accccgttgttgtctaaaaaaaatgcgtgctattttgctccttgatatgatgcagGTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG
         ttgtctaaaaaaaat  TA-rich tract