Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acattgcatctgttacttctttgaccaaataattttaatcttatcagtatgtttacattgcagagtgtttgcactgattgttgttccatgtttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCTTAGATGTGCCTCCTGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC

Basic information

species Zea mays
transcript GRMZM2G142984_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142984_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g38620.3 (Oryza sativa), 3'ss of exon 6
acattgcatctgttacttctttgaccaaataattttaatcttatcagtatgtttacattgcagagtgtttgcactga-ttgttgttccatgtttgtg----atagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCTTAGATGTGCCTCCTGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC
   || ||  |||   |||||| |      || |||| | ||||    |  |||  |   | |    ||||  || |  || || |  || ||||||    | |||||| |||||  ||||||||||||||||||| |  ||||||||||||||||| |||||||||||||| |||||||| || |||||||||||||| || ||
--ctttcaattgta--ttctttaattcttcaagttta-ttttatattcaactttgtaaaaccggacatttgtgctaaactgctgattgatatttgtgtcatacagATGAAATTGAACCTGATGTTTATGTTCCTGAGGTGGATATCCTGTCAGTCTTGGATGTGCCTCCTGGCAAAATGGGGCGTGTTATTGGCAGAAAAGGATC
















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|211452428|gb|FK953963.1|FK953963
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|211320745|gb|FL468785.1|FL468785
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|149107225|gb|EE189109.2|EE189109
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|32859979|gb|CD999660.1|CD999660
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|211412953|gb|FL027553.1|FL027553
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|16926376|gb|BM079444.1|BM079444
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|5070005|gb|AI737970.1|AI737970
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|166628372|gb|EG153265.1|EG153265
EST:     TCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: TCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|211383190|gb|FL437263.1|FL437263
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|67015787|gb|CO444536.1|CO444536
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|60344970|gb|DN211943.1|DN211943
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|37392421|gb|CF633460.1|CF633460
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|111189956|gb|EE288092.1|EE288092
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|16918764|gb|BM073885.1|BM073885
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
EST: gi|110531048|gb|EE035232.1|EE035232
EST:     CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTG                         ATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT
genomic: CTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCT

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: 46 (upstream exon), 49 (downstream exon)
Score: 61

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCTTAGATGTGCCTCCTGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 84

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCTTAGATGTGCCTCCTGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCTTAGATGTGCCTCCTGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 100

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAGCGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTCCCTGgtcagtatat ... tttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCTTAGATGTGCCTCCTGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatgtttacattgcagagtgtttgcactgattgttgttccatgtttgtgatagATGACATTGAGGCTGATGTTTATGTTCCTGAAGCCGATATCCTGTCAGTCTTAGATGTGCCTCCTGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC
                          cactgat  putative branch site (score: 100)
      tttacatt  TA-rich tract