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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttaaactttatttaaacgtttaagagtcaaaacttcacccatgagcgtttcaccgttttatagatttaataaccttggcaatcatttgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC

Basic information

species Zea mays
transcript GRMZM2G149520_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149520_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os09g34910.1 (Oryza sativa), 3'ss of exon 9
atgtttaaactttatttaaacgtttaagagtcaaaacttcacccatgagcgtttcaccgttttatagatttaataaccttggcaatca--tttgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC
                        || |||| |    |||    |  |   |||  | | || ||     | |    ||  |||||    ||||||||||||| ||||||||||||||||||||||||| ||| ||||||||||||  || ||| | |||| ||||||||||||||||||| |||||||| |||||||||||
-----------------------gtaggagtaa----ttcggttactatattttttctgctt-atgatggttaccttctaagcaatgtgttttgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATGTGAACAGAATAGAAAGGGAGTCTGGGGTCAAATTTGAACATATCTCTGC

upper sequence: GRMZM2G149520_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G38680.1 (Glycine max), 3'ss of exon 9
atgtttaaactttatttaaacgtttaagagtcaaaacttcacccatgagcgtttcaccgtt-ttatagatttaa--taaccttggcaatcatttgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC---
          | | | || | | ||     |     |||       ||  ||   |  |   |||| |||||||  | |   ||    |   ||  | ||||||||||||||| |||||||||||||||||||| || | |   |     |   |    ||| ||||||| ||||| || || |||||||| ||  | || ||   
---------gtatttctacaggatttgctattgg--cttactatgggattgtgatattggagttatcgatttaaggttatactgtggttttgtttttattcagGTAATACTGGGGTTGCTGTCATGCTTTATGATCCAAAA---AGATCTAACATACCTAGAATAGAAAGAGAGTCCGGTGTAAAATTTGAACACGTATCCGCCCC

upper sequence: GRMZM2G149520_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G29060.1 (Glycine max), 3'ss of exon 9
atgtttaaactttatttaaacgtttaagagtcaaaacttcacccatgagcgtttcaccgttttatagatttaataaccttggcaatcatttgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC---
       | |||||    |     ||   ||  |   ||     ||  | |||  |  | |||  || ||  ||| |  |||   |   ||  | ||||||||||||||| |||||||| ||||||||||| |||| | | |   |   | ||   ||| |||| || |||||||| || |||||||| ||  | |||||   
-----gtatctttacaggatttgctattggtttactattgtgatattggagtt--attgattttaaggtt--ata-ctgtggt--ttggtttttattcagGTAATACTGGGGTTGCTGTTATGCTTTATGA-CCCAAAAAGATCGAACATATC--TAGAATAGAGAGAGAGTCTGGTGTAAAATTTGAACACGTATCTGCTCC

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|31353684|gb|CD438041.1|CD438041
EST:     CCGGGATGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTG
genomic: CCGGGATGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatactaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTG




















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: 266

TGTGAACCTCCCCGGGATGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatactaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

TGTGAACCTCCCCGGGATGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatactaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

TGTGAACCTCCCCGGGATGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatactaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

TGTGAACCTCCCCGGGATGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatactaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagcgtttcaccgttttatagatttaataaccttggcaatcatttgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGCACAGTGTCAGCAGACTAGAAAGGGAGTCTGGGGTTAAATTTGAGCATATCTCTGC
                                                ttttc  CT-rich tract
              ttttatagatttaata  TA-rich tract