Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcaacgcactacacgctggcgccagatgggctgattcagatagcccattccgtctgtcgatgcactcttccgggggggccctgctgattgctaaatgggctgggctgtccacctgtttgttcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGGCGGGACGTCATCCTGGACGGCACGCTGTCCTGGGAGCCCT

Basic information

species Zea mays
transcript GRMZM2G070252_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070252_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g43010.1 (Oryza sativa), 3'ss of exon 6
gtacgcaacgcactacacgctggcgccagatgggctgattcagatagcccattccgtctgtcgatgcactcttccgggggggccctgctgattgctaaatgggctgggctgtccacctgtttgttcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGGCGGGACGTCATCCTGGACGGCACGCTGTCCTGGGAGCCCT
                             |     |||   |  | ||  || |   | | | |  ||      |    |||||  |||||    || ||   ||     ||   ||  |         ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||| ||||| || || ||||||||||| |
---------------------------gcaaaccttgaacaatgtggctaatccttacggcccaaacagagcagctaatgggccgggctgaca--tacatatacttacgggttggcccatgga-----atgcagGTGCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGTCGTGACGTCATCCTCGACGGTACCCTCTCCTGGGAGCCGT
















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|149099789|gb|EE185842.2|EE185842
EST:     CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTG                         GTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGG
genomic: CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGG
EST: gi|149101143|gb|EE187251.2|EE187251
EST:     CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTG                         GTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCT
genomic: CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCT
EST: gi|148952743|gb|EC898724.2|EC898724
EST:     CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTG                         GTCCACCAGTCGTCGACGGACGCGGCGTCG
genomic: CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCG
EST: gi|21760160|gb|BQ635701.1|BQ635701
EST:     CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTG                         GTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTG
genomic: CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTG
EST: gi|148950843|gb|EC896460.2|EC896460
EST:     CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTG                         GTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTG
genomic: CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTG
EST: gi|26457685|gb|CA829268.1|CA829268
EST:     CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTG                         GTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTG
genomic: CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTG
EST: gi|67020546|gb|CO449295.1|CO449295
EST:     CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTG                         GTCCACCAGTCGTCGACGGACGCGGCGTCNTCNCTGCTGGTGACGGCGCTG
genomic: CCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTG

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: 69

CGTGGTGGTGGAGGCGGACGCGTTCAAGGAGGCGGACGTCATCTACCGCGCCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGGCGGGACGTCATCCTGGACGGCACGCTGTCCTGGGAGCCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

CGTGGTGGTGGAGGCGGACGCGTTCAAGGAGGCGGACGTCATCTACCGCGCCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGGCGGGACGTCATCCTGGACGGCACGCTGTCCTGGGAGCCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

CGTGGTGGTGGAGGCGGACGCGTTCAAGGAGGCGGACGTCATCTACCGCGCCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGGCGGGACGTCATCCTGGACGGCACGCTGTCCTGGGAGCCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

CGTGGTGGTGGAGGCGGACGCGTTCAAGGAGGCGGACGTCATCTACCGCGCCATCAGCTCCATGGGCCACCACAACGACATGCTCCAGACGGCAGAGCTGgtacgcaacg ... tcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGGCGGGACGTCATCCTGGACGGCACGCTGTCCTGGGAGCCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggccctgctgattgctaaatgggctgggctgtccacctgtttgttcccgtgcagGTCCACCAGTCGTCGACGGACGCGGCGTCGTCGCTGCTGGTGACGGCGCTGAACGAGGGGCGGGACGTCATCCTGGACGGCACGCTGTCCTGGGAGCCCT
             tgctaaa  putative branch site (score: 74)
                                        tttgttccc  putative PPT
                taaat  TA-rich tract