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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagttttcttattgtgcatcattgtttgttgaaattgtttaaccgaatatatatctcacctaatatgtttttattattttccatgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC

Basic information

species Zea mays
transcript GRMZM2G418232_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 18
gtgagagttttcttattgtgcatcattgtttgttgaaattgtttaaccgaatatatatctcaccta-atatgt----ttttattattttccatgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
| | | | | | | | ||| ||| ||||||| | || ||||| | | || ||| || || || |||| | | ||||||||| ||||||||||||||||||||||||||||||||||| || || |||| |||| ||||||||||||||||| || ||| |||| || |||||
-------gtgagtgactacaaaacctattgggttcaaactgtttaattggctaattatctagcatgtatgtgtaacgttaatttcttccccattctttaagGTCAAAACTTCATACCTATGATGATGTTGTTGAGAGAGTTGCCCGTCAGCTTGGTGTGGATGATCCAGCGAAAATTCGTCTAACATCCCATAACTGCTAT

upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 22
-------------------------------gtgagagttttcttattgt-gcatcattgtttgt------tgaaattgtttaaccgaatatatatctcacctaatatgtttttattattttccatgc------ctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
|| ||| || ||||| | || || || || || | |||| ||| | | || | | |||| ||| | || ||||||| ||| |||| ||||||||||| || |||| ||| |||| ||||||| ||||| |||||| | | |||| ||||||| || ||||||||||||
gtaagcattgtgtaatttattggagcaaatcgttagatttaatatattgcagtatttttcttgagaggacatgtaagtatttatatattattatgcttagatttgcatcctcatcttatactccgtatatgaatttctagGTCAAGGCTCTATACATATGATGATGTGGTGGAGAAAGTGGCTCAACAACTTGGTTTGGATGATCCATCCATAATTAGGCTTACCCCTCACAATTGCTAC

upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 14
---------------------------------------gtgagagttttcttattgtgcatcattgtttgt-tgaaattgtttaaccgaatatatatctcacctaatatgttt----ttattattttccatgcctcaa------gGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
||| | | || ||| | | | || | || | || |||| | ||| | | | | | | |||| ||| |||| | || |||||| |||| ||| ||||||||||| || |||||||| || | ||||||| |||| |||||| | ||||| ||||||||||| ||||| ||||||
gtaagcatcttggaacttattgggggcaaattgttaagtttgatactatttagattttttactaacgtgcatatgtagttatttatagataattatgcttagcattttgtcctcagtcttatattttcccatatattaatttctagGTCAAGGCTTTTTACGTATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTCTGGATGATCCATCCAAAATACGGCTTACACCACACAACTGCTAC

upper sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
gtgagagtttt----cttat-tgtgcatcattgtttg--ttgaaattgtttaac-------cgaatatatatctcacctaatatgttt----ttattattttccatg------cctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
|| || | || |||| || ||| |||||| |||| | | ||||| | ||| ||| | | | | || |||| ||| |||| | || ||||||| |||| ||| ||||||||||| || |||||||| || | ||||||| ||||| ||||| | ||||| ||||||||||| ||||| ||||||
gtaagcatcttgaaacttacatgggcaa-attgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtcttatactttcccatatgttaacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC

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|78113609|gb|DV532000.1|DV532000
EST:     TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATT                         GTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACT
genomic: TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATTgtgagagttt ... atgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACT




















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), 44 (downstream exon)
Score: 91

TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATTgtgagagttt ... atgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC


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

TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATTgtgagagttt ... atgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 39

TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATTgtgagagttt ... atgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

TTCCGGTCTTTGGAGAAACCAAAGGATGATGATTTTTCTTTGGAATTgtgagagttt ... atgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaccgaatatatatctcacctaatatgtttttattattttccatgcctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC
                    acctaat  putative branch site (score: 40)
 ttttccat  putative PPT
 aatatatatctcacct  TA-rich tract