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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttactatctcgaaatgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG

Basic information

species Zea mays
transcript GRMZM2G149321_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g40340.1 (Oryza sativa), 3'ss of exon 16
gtaatttactatctcgaaatgt--tctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG
|||||||   ||||  |||  |  | ||  | | || |||||| |||  | |  |    ||||||  | ||||| |||| |||||| ||||||||||||||||| |||||||| |||||||||||||||||||| |||  ||| |||||  ||||    |||||||| || || || |||||   |
gtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttg--ggctaattatgtgtttatgtatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTATTACTGACCGTTTGGCTGCG---GTTCCTTCGTCTTCACCTAATTCAGAG

upper sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g40340.2 (Oryza sativa), 3'ss of exon 16
gtaatttactatctcgaa--atgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG---
|||||||   ||||  ||  ||  | ||  | | || |||||| |||  | |  |    ||||||  | ||||| |||| |||||| ||||||||||||||||| |||||||| |||||||||||||||||||| |||  ||| |||||  ||||    |||||||| || || || |||||   |   
gtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttg--ggctaattatgtgtttatgtatttaaaagcagTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTATTACTGACCGTTTGGCTGCG---GTTCCTTCGTCTTCACCTAATTCAGAGGAG
















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|67016491|gb|CO445240.1|CO445240
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG                         CTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
EST: gi|211428993|gb|FL402814.1|FL402814
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG                         CTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
EST: gi|31364305|gb|CD448660.1|CD448660
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCATGACAG                         CTCCCTGTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
EST: gi|211266310|gb|FL390568.1|FL390568
EST:     TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG                         CTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT
genomic: TCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCAT

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: 384

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 296

GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttact ... ttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcagCTCCCTCTTTACAAATTCAAATTGGTTCACATTTGATGGAGAGAGAGGCATTGATGATCGTTTATCTGCCTCTGTTCCTTCATCATCCCCCAATTCTCTG
                   ggctgat  putative branch site (score: 296)
     agtttttat  TA-rich tract