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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgcatattcctcttcccttttgtgcagttttgtatttgtccgtttcaatgcccgggccgaactgtggtgctaatgttttcgttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGTTGAGAAAAGCTTGGATTTTCTTAAGAG

Basic information

species Zea mays
transcript GRMZM2G100652_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------------------gtacatgcatattcctcttcccttttgtgcag----ttttgtatttgtccgtttcaatgcccg---ggccgaactgtggtgctaatgttttcgttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGTTGAGAAAAGCTTGGATTTTCTTAAGAG
                                                               |||  |    | |||| | | || |||  ||    ||||| | |   |  ||  | | || |     | | |   |  | ||     |||   |  | ||| || |||||||||||||| || ||| || | |||||||| || || ||||||||||||||||| || |||||||||||
gtatgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgctaaattgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGTTGAGAAAAGCTTAGACTTTCTTAAGAG
















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|71425523|gb|DR806728.1|DR806728
EST:     GAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC                         GAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT
genomic: GAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT
EST: gi|211491629|gb|FL429938.1|FL429938
EST:     TCCGCAACATGGAAATGCGTTCAAGGCTAAC                         GAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT
genomic: TCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT
EST: gi|94472299|gb|EB701257.1|EB701257
EST:     AAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTNCA-GGCTAAC                         GAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT
genomic: AAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTT-CAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT
EST: gi|211368674|gb|FL393824.1|FL393824
EST:     TCCGCAACATGGAAATGCGTTCAAGGCTAAC                         GAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT
genomic: TCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGT

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), 49 (downstream exon)
Score: 83

CCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGTTGAGAAAAGCTTGGATTTTCTTAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

CCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGTTGAGAAAAGCTTGGATTTTCTTAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 47

CCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGTTGAGAAAAGCTTGGATTTTCTTAAGAG


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

CCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcat ... gttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGTTGAGAAAAGCTTGGATTTTCTTAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtccgtttcaatgcccgggccgaactgtggtgctaatgttttcgttggagcagGAATGGTGAACCAGAAAAGCCACTTGTATTTTATGTTGGACGCTTAGGAGTTGAGAAAAGCTTGGATTTTCTTAAGAG
                                tgctaat  putative branch site (score: 48)
                                        ttttcgtt  CT-rich tract
                                   taatgtttt  TA-rich tract