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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatcttttaacaaccgctccctaccatcctgtaattccagaccattatttttgtattctcattgttactttaaaatatgaatataattcctgattttcaaccatatttactgatagatttgctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA

Basic information

species Zea mays
transcript GRMZM2G033592_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 12
gtatgtcatcttttaacaaccgctccctaccatcctgtaattccagaccattatttttgtattctcattgttactttaaaatatgaatataattcctgattttcaaccat-atttactgatagatttgctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA
                                              |  |  | |||  ||      ||||||||  |   ||| || | ||| |   ||| | ||  || ||  | |   |   || ||   |  ||||||||| |||| ||||||||||| || ||||||||||||||||  || ||||||||||| || || ||  ||||||| |||   |||   || ||||||
-------------------------------------------gtaattaacactttgttagctc--ttgttactaaattctataaaga-aatacaatattctaaagaattatgcattctcaatcttacttgcttcagGTGCATGCTACATAACTTTGGTGGCAATATTGAAATGTATGGCACTCTGGATTCAATTTCTTCAGGGCCTGTTGATGCTCGTGTCAGTGCAAACTCAACA

upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G13690.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatgtcatcttttaacaaccgctccctaccatcctgtaattccagaccattatttttgtattctcattgttactttaaaatatgaatataattcctgattttcaaccatatttactgatagatttgctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA
                                                   ||| || ||  ||||| | |   | | |    ||| |  | ||    ||||| |    | |||| | |||         | || ||||||||| | ||||| ||||| || |||||||||||||||||    |||||||||||||| || || ||  ||||||| |||   ||  | |||||||| 
--------------------------------------------------gtatatt-gttgtctcagtttccttcttatgcctgagt-cagttgt--atttttacgtgtttttatt-ataatcggatgaattccagGTGCATGCTTCACAATTTTGGAGGCAACATTGAAATGTATGGTGCTCTTGATTCAATTTCTTCAGGACCAGTTGATGCTCGTGTTAGCAAAAATTCAACC

upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv13s0064g00370.t01 (Vitis vinifera), 3'ss of exon 12
----------------------------gtatgtcatcttttaacaaccgctccctaccatcctgtaattccagaccattatttttgtattctcattgttactttaaaatatgaatataattcctgattttcaaccatatttac--tgatagatttgct--caatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA
                             ||| ||||   || | |     |    |   ||  |  |       |  ||| | ||| ||| |   | ||  |||    | |        ||  |   |  |||  ||  ||||  ||  |  |||  |  |||   ||||| ||||| || ||||||||||| || |||||||||||||||||| | ||| || |||| ||||| ||  ||||||| || |  ||| | |||||||| 
gtaaccagctctttcaaagaagtagctactatttcataccttgagatagagttttcatgttcaagagaaatttt-ctcttaatcttgcattatttatcttcttttcttttttagtctgggtttatctgtaacaaatatgcttaccatgtcaatttttgttacaaatcagGTGTATGTTGCATAACTTTGGTGGAAATATTGAAATGTATGGCATATTAGATGCAGTTTCTTCTGGTCCAGTTGATGCTCGCATCAGTAAAAATTCAACC

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|91873217|gb|EB403174.1|EB403174
EST:     AAGCCCATTAGGAAAGTGTCCTCTCAGTTGTACGGCGTACCATACATCTG                         GTGCATGTTACACAACTGTGGTGGGAACATTGAAATGTATGGCATACTTGA
genomic: AAGCCCATTTGGAAAGTGTCCTCTCAGTTTTACGGCGTACCATACATCTGgtatgtcatc ... ctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGA




















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), 42 (downstream exon)
Score: 56

ACTCTGTTCCAATTGGTAAGATGATAGTTCTCGATTTATTTGCTGATGTCAAGCCCATTTGGAAAGTGTCCTCTCAGTTTTACGGCGTACCATACATCTGgtatgtcatc ... ctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 76

ACTCTGTTCCAATTGGTAAGATGATAGTTCTCGATTTATTTGCTGATGTCAAGCCCATTTGGAAAGTGTCCTCTCAGTTTTACGGCGTACCATACATCTGgtatgtcatc ... ctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98

ACTCTGTTCCAATTGGTAAGATGATAGTTCTCGATTTATTTGCTGATGTCAAGCCCATTTGGAAAGTGTCCTCTCAGTTTTACGGCGTACCATACATCTGgtatgtcatc ... ctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 57

ACTCTGTTCCAATTGGTAAGATGATAGTTCTCGATTTATTTGCTGATGTCAAGCCCATTTGGAAAGTGTCCTCTCAGTTTTACGGCGTACCATACATCTGgtatgtcatc ... ctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatataattcctgattttcaaccatatttactgatagatttgctcaatctagGTGCATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACA
                               tactgat  putative branch site (score: 57)
                                         tttgctc  putative PPT
                          atatttact  TA-rich tract