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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacatgatataatcaattttgttccagaattattatctcaagacatttgtttcagttcacatcatcacaaacattaacttcccacttgcccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT

Basic information

species Zea mays
transcript GRMZM2G024690_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024690_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 3'ss of exon 11
gttacatgatataatca-attttgttccagaattattatctcaagacatttgtttcagttcacatcatcacaaacattaacttcccacttgcccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT
|||||||  | |  |   ||||| ||   |  |   |   | | |  || ||       |   ||||| | | | | ||  |||| ||||     | || |||| |||||||| || ||||| |||||||| ||||| ||||| ||||| |||||||| ||||||| ||||||||||||||||
gttacattctctcttttcattttattattgtttaccttattaatgttatgtgcactctattttatcataatata-actattttcctacttattatctttcagGTATGGAGGCTCCAAGCAGCTTTGGGAGAGCAATCAGAAATTACCAAATGTACCAAGCAGGAATTTGAAAGGCTTCAAAAT
















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|20300032|gb|BQ162975.1|BQ162975
EST:     ATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAG                         GTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGT
genomic: ATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAGgttacatgat ... ccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGT
EST: gi|33098379|gb|CF058339.1|CF058339
EST:     ATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAG                         GTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGT
genomic: ATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAGgttacatgat ... ccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGT

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: 48 (upstream exon), 48 (downstream exon)
Score: 76

GTACAATACATTTTGTGGCTATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAGgttacatgat ... ccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 92

GTACAATACATTTTGTGGCTATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAGgttacatgat ... ccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

GTACAATACATTTTGTGGCTATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAGgttacatgat ... ccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

GTACAATACATTTTGTGGCTATCCACCAGAAGTGGTTAGGAAAATGCCTAAAAAGGACCTTGCAGAAGAGgttacatgat ... ccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtttcagttcacatcatcacaaacattaacttcccacttgcccacctttagGTTTGGAGGCTGCAGGCAGCGTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT
                           cattaac  putative branch site (score: 94)
                                 cttcccacttgccc  CT-rich tract
                        aaacattaa  TA-rich tract