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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttcgatctttctcactaagcaaatttgcttccaatagtactgctttaagtgttcgccctgctatcattgatcctctttcttaaacattttctgttgttcattttgtttcgatagtttaaattttccttttcggatatgacggtcttttccttttcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG

Basic information

species Zea mays
transcript GRMZM2G174343_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174343_T07 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g04660.1 (Oryza sativa), 3'ss of exon 8
gttgttcgatctttctcactaagcaaatttgcttccaatagtactgctttaagtgttcgccctgctatcattgatcctctttcttaaacattttctgttgttcattttgtttcgatagtttaaattttccttttcggatatgacggtcttttccttttcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG
                                                     | |||  | | ||       || |  |  |  |   ||     |||  ||  ||  ||  |  | ||| ||| |||||||| | |  || |  ||| |||||||||  ||| ||||||  ||||||||||||||||||||||||| || || ||||||| ||| || ||  |||| ||| ||| ||| |||||     |||  ||||   ||| 
---------------------------------------------------gtttttcagctttcttaagcaaattcgttcaccaaggaatg----gtttctctcttccttaagcaaatttgaatattcctttttgaaagtggc--tctcttccttttcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCAACTCCCACAATGCAGAAAGCCAGCAGTCAGTGTGTGGGCATCATGTTGA
















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|71767864|gb|DR965801.1|DR965801
EST:     GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAG                         GTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA
genomic: GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAGgttgttcgat ... tcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA
EST: gi|74242710|gb|DT650624.1|DT650624
EST:     GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAG                         GTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA
genomic: GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAGgttgttcgat ... tcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA
EST: gi|76014150|gb|DT941320.1|DT941320
EST:     GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAG                         GTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA
genomic: GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAGgttgttcgat ... tcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA
EST: gi|71326098|gb|DR799728.1|DR799728
EST:     GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAG                         GTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA
genomic: GGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAGgttgttcgat ... tcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAA

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 7

GATTTATCATGGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAGgttgttcgat ... tcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG


Block sizes: 18 (upstream exon), 45 (downstream exon)
Score: 6

GATTTATCATGGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAGgttgttcgat ... tcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 12

GATTTATCATGGCAGTGCTATGTTACCTGCATTTCTTTCCTCCTCCATACCATGATCAAGgttgttcgat ... tcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatagtttaaattttccttttcggatatgacggtcttttccttttcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG
                               cggtcttttccttttc  CT-rich tract
      tttaaattttcctttt  TA-rich tract