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

...gtttaaaattcttcctttttcgtatgcatacatatatgtagcctgtgccaacccttgaatgatgaacatgtctgacaatatccaccatatttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTGCATGGCCTTGAGTTGGCATTGGATGAGATCTCTTATGATTTGGCTGTAT

Basic information

species Glycine max
transcript GLYMA06G19940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G19940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G078725_T01 (Zea mays), 3'ss of exon 3
-gtttaaaattcttcctttttcgtatgcatacatata---tgtagcctgtgccaacccttgaatgatgaacatgtctgacaatatccaccatatttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTGCATGGCCTTGAGTTGGCATTGGATGAGATCTCTTATGATTTGGCTGTAT
   | ||||     | ||||  ||    |  || |||   | ||| |    | ||   |   |     |    |||||| | |   || | | | ||| | |||||||| |||||||  || || || || |||||| |||| |||||  | |||||||| || ||| |||| |||||||||||||||  |||||||||  | |
acatgaaaacaaaacgttttgtgtcataaggcacatagggtttagtcatcacgaagttt---actggaagtgagtctgaaatttgtcatcctttatttat-cagAAATTTATGGGGAAGTCCGAGAACGGTATGCGTTCTTTGGAGACAAGAGTGCATGGGCTGGAGATGGCTTTGGATGAGATCTCTCGTGATTTGGCCTTCT
















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|58018233|gb|CX704975.1|CX704975
EST:     TTCAAA-TGAGAAAGCAGCAGTCTAGTCTGCTTGATCTTGTACAG                         AAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
genomic: TTCAAATTGAG-AAGCAGCAGTCTAGTCTGCTTGATCTTGTACAGgtttgttcca ... ttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
EST: gi|7283430|gb|AW596038.1|AW596038
EST:     AATTAGTTCAAATTGAGAAGCAGCAGTCTAGTCTGCTTGATCTTGTACAG                         AAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
genomic: AATTAGTTCAAATTGAGAAGCAGCAGTCTAGTCTGCTTGATCTTGTACAGgtttgttcca ... ttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
EST: gi|13477635|gb|BG507437.1|BG507437
EST:     AATTAGTTCAAATTGAGAAGCAGCAGTCTAGTCTGCTTGATCTTGTACAG                         AAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
genomic: AATTAGTTCAAATTGAGAAGCAGCAGTCTAGTCTGCTTGATCTTGTACAGgtttgttcca ... ttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
EST: gi|192328733|gb|FK022533.1|FK022533
EST:     AATTAGTTCAAATTGAGAAGCAGCAGTCTAGTCTGCTTGATCTTGTACAG                         AAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
genomic: AATTAGTTCAAATTGAGAAGCAGCAGTCTAGTCTGCTTGATCTTGTACAGgtttgttcca ... ttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
EST: gi|193476308|gb|FK443425.1|FK443425
EST:     GATCTTGTACAG                         AAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG
genomic: GATCTTGTACAGgtttgttcca ... ttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccaacccttgaatgatgaacatgtctgacaatatccaccatatttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTGCATGGCCTTGAGTTGGCATTGGATGAGATCTCTTATGATTTGGCTGTAT
                        gtctgac  putative branch site (score: 3)
                                          tattttttt  putative PPT
                                         atatttttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaaaattcttcctttttcgtatgcatacatatatgtagcctgtgccaacccttgaatgatgaacatgtctgacaatatccaccatatttttttacagAAATTCATGGGGAGCTCTGAAAATGGAATGCGTACTTTAGAGACTCGTGTGCATGGCCTTGAGTTGGCATTGGATGAGATCTCTTATGATTTGGCTGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC