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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgctttcccctcaatccaacacctgctcattacttggttccagtcacaagattaaaactcgtatgcaatcgaaccactgcag

Basic information

species Zea mays
transcript GRMZM2G115245_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 29
TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgctttcccctcaatccaacacctgctcattac--ttg-gttccagtcacaagattaa-aactcgtatgcaatcgaaccactgcag--------------
||||||| ||||||||||||||||||||||| ||||| || ||||||||||||||||| || || || ||||||||||||||||||||||||||   ||| | | || || |  |  ||  |||| |  |||  |   ||  | ||| ||    |  |  | ||  |  |   |     |              
TTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatttttctcccattcaacaatttgtacatttcagttgcatgttagctataagcttcttgatccacaagctttaaatttatgttggtgcaatgatcgcag

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA06G16110.2 (Glycine max), 5'ss of exon 29
TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgctttcccctcaatccaacacctgctc---attacttgg----ttccagtcacaagattaaaactcgtatgcaatcgaaccactgcag-------
| ||||| ||||||||||| ||||||||| | |||||||| || |||||||||||||| || || || ||||| ||||||||||| |||| || | | |||   | |||   | | |        ||| |||||     |  |||    |||||     |  || | |  |  |  | | |||       
TGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACCAGgtatgtt-cattcagttaaatattatatcattgagggattgcttggggggctagagttctcagatttttggttttaag-aggcacaatatttcagtattaaa

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA04G38800.2 (Glycine max), 5'ss of exon 13
TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgctttcccc-----tcaatccaacacctgctcattacttgg----ttccagtcacaagattaaaactcgtatgcaatcgaaccactgcag----
| ||||| ||||||||||| ||||||||| | |||||||| || |||||||||||||| || || || ||||| |||||||||||||||| || |  |||         | |   ||        | ||| |||||     |  |||    |||||     |  || | |  |  | |  | |||    
TGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACAAGgtatgttcatttagtgaaatattatatcattgaggattgattgcttggggggctagagttctcagatttttggttttaag-aggcacaactttacagtatt

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT5G63960.2 (Arabidopsis thaliana), 5'ss of exon 29
TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct-ttcccctcaatccaacacctgctcattacttggttccagtcacaagattaaaactcgtatgcaatcgaaccactgcag--------------------
|  |||| || ||   | | ||||||||||| |||||||| ||||||||||| ||||| ||||| || || || ||  | ||||| |||||||||  | ||    || ||   |       | |  | |   || |||     | ||  |   ||  || ||||       ||| |                     
TGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAGgtttgcttatatttttatcgatatcaatttcttttagaaatc--tttcagcaggtaaat--aggttctgatccaatttcctttctggatttcttattggtcttttacag

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ15224 (Selaginella moellendorffii), 5'ss of exon 28
TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgctttcccctcaatccaacacctgctcattacttggttccagtcacaagattaaaactcgtatgcaatcgaaccactgcag
|    ||  |||||  ||| ||||| ||||| ||||| |||||||||  ||||||||||||| | || || |||||| | |||||||||||     || |        |    |  |  || |  |     ||       ||                                  
TGAGGGATTTGGAGCAGCTATTTGGAAGGCTGTGGACTCAATGCCAGCGGTGCCAAGGATCTTTACATCAAGACGTTTTGTGCACAAGgttgagcactgtagtagtgtttatgcctcaactaacaaaggcattgtgtctgcag---------------------------------

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ15982 (Selaginella moellendorffii), 5'ss of exon 28
TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgctttcccctcaatccaacacctgctcattacttggttccagtcacaagattaaaactcgtatgcaatcgaaccactgcag
|    ||  |||||  ||| ||||| ||||| ||||| |||||||||  ||||||||||||| | || || |||||| | |||||||||||      | |        |    |  |  || |  |     ||    |  ||                                  
TGAGGGATTTGGAGCAGCTATTTGGAAGGCTGTGGACTCAATGCCAGCGGTGCCAAGGATCTTTACATCAAGACGTTTTGTGCACAAGgttgagcattgtagtagtgtttatgcctcaactaacaaaggcattgtgtttgcag---------------------------------

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|17921941|gb|BM259592.1|BM259592
EST:     CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG                         TCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
genomic: CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
EST: gi|101399027|gb|EB821386.1|EB821386
EST:     CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG                         TCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
genomic: CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
EST: gi|17921796|gb|BM259447.1|BM259447
EST:     CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG                         TCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
genomic: CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
EST: gi|211441104|gb|FL033100.1|FL033100
EST:     CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG                         TCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
genomic: CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
EST: gi|17921470|gb|BM259121.1|BM259121
EST:     CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG                         TCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
genomic: CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
EST: gi|17921753|gb|BM259404.1|BM259404
EST:     CAATGCCTGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG                         TCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC
genomic: CAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGAC

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), 48 (downstream exon)
Score: 180

TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGACCGAAGCTAGGCTGCAGCTTGATCGGTGGGACTTCTGAGCTTGGAAATTC


Block sizes: 42 (upstream exon), 41 (downstream exon)
Score: 19

TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGACCGAAGCTAGGCTGCAGCTTGATCGGTGGGACTTCTGAGCTTGGAAATTC


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 22

TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGACCGAAGCTAGGCTGCAGCTTGATCGGTGGGACTTCTGAGCTTGGAAATTC


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 25

TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgct ... accactgcagTCGGGATTGCCCCATTTTCTATCGGCGAAGGAAGGCACAGAAGGATATGACCGAAGCTAGGCTGCAGCTTGATCGGTGGGACTTCTGAGCTTGGAAATTC