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'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctcattccctttcagcagatggaccgcattgttgtcatgctctggttccactcatatattgcttgttgggtgcccgtctttcacacggtacca...

Basic information

species Zea mays
transcript GRMZM2G162445_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162445_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 5'ss of exon 3
GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaat-gtctcattccctttcagcagatggaccgcattgttgtc--atgctctggttccactcatatattgcttgttgggtgcccgtctttcacacggtacca
|| |||||||| || ||||| ||||||||||||||||||||||| |||||||| ||||||||||| || ||||||||||| |||||||||||||| ||||||||| |  ||   |   ||  | | ||   |    |||||     ||  || |||| || |    |  |    |||        |   || |     ||   
GGATTCTCGGGGCCCTTCGGCTTCCACAGGGTCACGCCCAGGGACCTCATGTCGTCCTTCATCGGGACTATGGTCTGCGTCGAGGGCATCGTCACGAAATgtaattgaatctccctaattttggacataatctagtttgttcatagattttccggttgcagttggctgatctgggtttaacttgtggtctttatgattta---

upper sequence: GRMZM2G162445_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G25980.1 (Glycine max), 5'ss of exon 3
GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctcattccctt-tcagcagatggaccgcattgttgtcatgctct--ggttccactcatatattgcttgttgggtgcccgtctttcacacggtacca
|| ||    || || || |  |  | | | |||||||||||||||||  | ||    ||||| ||  |||||||||| ||||||||||| ||||||||||||||  |  |  | |||| |       | | ||   || | ||  |  |||  ||||  | | ||  | |||        |  |      | |   | ||   
GGATTTGAAGGCCCTTTTGTTTCTCGCCGTGTCACGCCCAGGGATCTTCTCTCTCAATTCATAGGTTCCATGGTCTGTGTTGAGGGCATTGTCACCAAATgtaaaattactctgccttattttttttttgtcctttttttagttgttgtctatggtttaaatgattgactgcacccaatttctcatgaaattaggtgata---

upper sequence: GRMZM2G162445_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 5'ss of exon 3
GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtc-tcattccctttcagcagatggaccgcattgttgtcatgctctggttccactcata---tattgcttgttgggtgcccgtctttcacacggtacca
|| ||    |||   || |  |  | |   || || || || || ||  | ||    || || ||  | |||||||| ||||||||||| ||||||||||||||  || |||||  |  ||      |   |     |  |||     |   |||  ||  | |   | |||    |  |   |  |  || |   | |     
GGTTTTGAAGGTTATTTTGTTTCTCGCGTTGTTACTCCTAGAGAGCTTCTCTCTGATTTTATTGGATCTATGGTCTGTGTTGAGGGCATTGTCACCAAATgtaagctcatcattttcactctattcctctgcttttcttctgtttcctttgtgttttacgtagaagattttgaacctctgacacatgctttgctttcag-----

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|211495775|gb|FL137513.1|FL137513
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
EST: gi|211495774|gb|FL137512.1|FL137512
EST:     TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
genomic: TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
EST: gi|211498656|gb|FL137521.1|FL137521
EST:     TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
genomic: TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
EST: gi|148956698|gb|EC902568.2|EC902568
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
EST: gi|211498653|gb|FL137518.1|FL137518
EST:     TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
genomic: TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
EST: gi|211498654|gb|FL137519.1|FL137519
EST:     TTCATCGGCACCATGGTTCTGCGTTGAGGGCATCGTCACCAAAT                         GTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
genomic: TTCATCGGCACCATGG-TCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
EST: gi|211495776|gb|FL137514.1|FL137514
EST:     TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA
genomic: TTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGA

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: 117

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 24

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 14

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 9

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaatgtctc ... aaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGG