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'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatataatatatattctctatgatatgtttgcgtacttgtgacagttagtgatatctttgttacaccagcttactctttttgtttttaaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATCCCAACATTGCCATTTGGCTAGCTGATGCCCCTCAATCTGTCTTAGAAGT

Basic information

species Glycine max
transcript GLYMA17G03920.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 5
--gtaata-taatatatattctctatgatatgtttgcgtacttgt-gacagttagtgatatctttgttacaccagcttactctttttgtttttaaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATCCCAACATTGCCATTTGGCTAGCTGATGCCCCTCAATCTGTCTTAGAAGT
   | ||  |  | |   || |  |||| |      |  | |||| | || |    || ||  ||| |  |||   |   || | |  | |||      ||||||  || ||||| || |||||||||||||| |||||||| ||| | ||||| |||||||| || ||| | |||||||| |||||||| ||  |||||||
gtatgattctcttttcctttttgcatgaaaaaaggccacatttgttggcattgtaagaaatgcttgct-tacctaatgtttcctctcctctttg-----cagCTAACAAATGCAGCTTAGAGATAGATTACAAGCAATTTATTTATATACATCCAAACATTGCTATATGGTTGGCTGATGCACCTCAATCGGTGCTAGAAGT

upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 5
gtaatataatatatattctctatgatatgtttgcgtacttgtgacagttagtgatatctttgttacaccagcttactctttttgtttttaaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATCCCAACATTGCCATTTGGCTAGCTGATGCCCCTCAATCTGTCTTAGAAGT
           ||| |   || | | ||  |   ||     || ||   |   |  |||||| | | |   |       | || ||||       ||||||  ||||| ||  |||| ||||| ||||| || ||||| ||| | ||||| ||||||||||| ||| | |||||||| |||||||| ||  | |||||
----------gtatgtctgct-tcacattctctggt-----tggcatgaaacaaggtctttgcttctctgacccttatctatttttttcg-----cagCTAACAAGTGTAGCCTGGAAATAGACTACAAGCAGTTTATTTATATACATCCAAACATTGCCATCTGGTTGGCTGATGCGCCTCAATCGGTGCTTGAAGT

upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------gtaatataatatatattctctatgat-atgtttgcgtacttgtgacagttagtgat--atctttgttacaccagcttactctttttgtttttaaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATCCCAACATTGCCATTTGGCTAGCTGATGCCCCTCAATCTGTCTTAGAAGT
                                 || | ||  || |  |   || | || ||     | |   |     | |||||     || ||| ||| |    || |   | |     | || |||| |||||  ||||| ||||||||||| ||||||||||| || |||||| | |||||||| ||||| || ||||| ||||||||||||||||||||| | || ||
gtagaatatctccttgtgcttcgtttttaacatgtgaaattgtaaaagtgaactgtcattatcccctcctggctcatctatttagttgctcatgttttttatatggactaa---tctaatactgtatatgc-agCTAACAAGTGTAGTTTGGAGATTGATTACAAACAGTTCATCTATATCCATCCCAATATTGCTATCTGGCTGGCTGATGCCCCTCAATCTGTCCTTGAGGT

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|208320062|gb|GE116393.1|GE116393
EST:     GTCTGGCTGATAAATGAGATGGCGTCAG                         CTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATC
genomic: GTCTGGCTGATAAATGAGATGGTGTCAGgtaatataat ... taaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATC
EST: gi|193605481|gb|FK558643.1|FK558643
EST:     TGAACATCGGGACAAGGAATATGTCTGGCTGATAAATGAGATGGTGTCAG                         CTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATAGTTCAT
genomic: TGAACATCGGGACAAGGAATATGTCTGGCTGATAAATGAGATGGTGTCAGgtaatataat ... taaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTAT-GTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagttagtgatatctttgttacaccagcttactctttttgtttttaaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATCCCAACATTGCCATTTGGCTAGCTGATGCCCCTCAATCTGTCTTAGAAGT
                          agcttac  putative branch site (score: 3)
                            cttactctttttgttt  CT-rich tract
                             ttactctttttgtttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatataatatatattctctatgatatgtttgcgtacttgtgacagttagtgatatctttgttacaccagcttactctttttgtttttaaatgccagCTAGTAAGTGCAGTTTGGAGATAGATTACAAACAATTTATCTATGTTCATCCCAACATTGCCATTTGGCTAGCTGATGCCCCTCAATCTGTCTTAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT