Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaattctgcttttgggttattggcttttgtttggatgttggttgttgaatttggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG

Basic information

species Glycine max
transcript GLYMA17G10170.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G10170.3 (Glycine max), 3'ss of exon 2
lower sequence: AT3G48100.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtgaattctgcttttgggttattggcttttgtttggatgttggttgttgaatttggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG
|||| | |||       ||| |||      |||||   |   |       |  ||||||||| |||     || || ||||||    || |  ||  ||  | | ||| ||||| | |||||||||||||| || ||||| |||||||| ||||||||| |||| ||||| ||||| 
gtaa-taaatctgatcattgtgtttaatatttttgagagtgagaatccattcaaatttggtg-ttaaaagatttttggtttga--aattata-ttttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA

upper sequence: GLYMA17G10170.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G74890.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gtaa-gtgaattctgcttttgggttattggcttttgtttggatgttggttgttgaatttggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG
       || ||| ||      |||    | | |    |  |||   | || |||  |  |  ||  | |||| |         |||      || || | ||||  | | || || ||  | ||| ||||||||||||| ||||||||  | |||||||||||| | |||||||| ||||| 
gtttcacaatgtggatcaaaagtttaacctttagaggatgattttattatttgtttattga--tgccgtttatatgaaca---attttgcaaattttgataacagGATTTGAAAGTGAACTTGATAGTGACGGATTATTCAATGCCGGGACTAACAGGATATGAACTCCTCAAGAAGATCAAA

upper sequence: GLYMA17G10170.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtgaattctg--cttttgggttattggcttttgtttggatgttggttgttgaatt--tggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG
| || | ||    |  ||||| | || |    ||||| ||  || |      ||   ||  |  || ||   |  ||| |  | | | ||||| |  ||  || || | ||||| ||||| || |||||||| ||||| ||||| ||||||||||| ||||| || |||||||| ||||||
gcaaataaacagaggtctttttgtttttccttttttgattaaat-tcaaagatttctttaatactgtttggatgattgat-atctcaatggtt-tccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG

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|192312818|gb|FK005430.1|FK005430
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|213620080|gb|DB967451.1|DB967451
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|209713249|gb|BW681788.1|BW681788
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|192309041|gb|FK001817.1|FK001817
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|193730031|gb|FK667847.1|FK667847
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|192294700|gb|FG986549.1|FG986549
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|18732668|gb|BM527175.1|BM527175
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|193590792|gb|FK545897.1|FK545897
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
EST: gi|192312819|gb|FK005431.1|FK005431
EST:     CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGAT                         AGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA
genomic: CTCTTCAGTATCTTGGGTTGGAGGGAGAGAACGGTTCTCTTGGGTTTGATgtaagtgaat ... gtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgttgaatttggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG
                                 gtttgat  putative branch site (score: 5)
      ttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaattctgcttttgggttattggcttttgtttggatgttggttgttgaatttggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA