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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcacttctgccagtggttcatatgttctctaaatgtttagtcgattgtattgatgtattctaatctactcgtgctagggattgtgctaactttttctctctcattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGG

Basic information

species Zea mays
transcript GRMZM2G120175_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g43790.2 (Oryza sativa), 3'ss of exon 5
gtaatgtcacttctgccagtggttcatatgttctctaaatgtttagtcgattgtattgatgtattctaatctactcgtgctagggattgtgctaactttttctctctcattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGG
|||||||||||| | |||    ||    | |||| |   |||||  |     || ||||   | | || ||| |     |||  | |  ||||||  |||   |      ||||||||| ||||||||||||||||||||||||||  ||||| | || |||||||| ||||| || ||  ||||||||||||||||||||||| ||||| | ||||
gtaatgtcacttataccatcaattgcagtattct-tggttgttttat-----gttttgaatgactttactctcc-----ctaatggtc-tgctaatgtttgtccata---tattcagGTAATGAGTGTTAAAGCTCTTGGTACATCCTTAAAGTTGACGTTTGAGGGGACAAATCAGTTGGTATATCCAGAGACTTGGTTCTTTGTGCTTATAGTGG
















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|5895870|gb|AW037116.1|AW037116
EST:     CCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCG                         GTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGA
genomic: CCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCGgtaatgtcac ... cattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGA
EST: gi|76287457|gb|DV027025.1|DV027025
EST:     ATTTGCTTTTTGATGGGCTCTCTTTCG                         GTTATGAGTGTAAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGA
genomic: ATTTGCTCTTTGATGGGCTCTCTTTCGgtaatgtcac ... cattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGA
EST: gi|76281094|gb|DV020662.1|DV020662
EST:     CCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCG                         GTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGA
genomic: CCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCGgtaatgtcac ... cattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGA

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: 58

TGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCGgtaatgtcac ... cattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 188

TGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCGgtaatgtcac ... cattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 226

TGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCGgtaatgtcac ... cattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

TGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGCCATTTGCTCTTTGATGGGCTCTCTTTCGgtaatgtcac ... cattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctaatctactcgtgctagggattgtgctaactttttctctctcattattcagGTTATGAGTGTTAAAGCTCTTGGTACATCACTAAAGCTTACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGG
                           tgctaac  putative branch site (score: 51)
                                 ctttttctctctcatt  CT-rich tract
                              taacttttt  TA-rich tract