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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatatatattctttgctaaacctttgactagttttctgttattgcctacttttacgtgcacatcctatatcgtgtggattgtattttatagggatgatttttggaagctaatctgatctaatctgttttttttgcctttttgattaaatattctaacttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAAGTGGTTAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAA

Basic information

species Glycine max
transcript GLYMA07G06230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g12170.2 (Oryza sativa), 3'ss of exon 3
gtaaggatatatattctttgctaaacctttgactagttttctgttattgcctacttttacgtgcacatcctatatcgtgtggattgtattttataggg-atgatttttggaagctaatctgatctaatctgttttttttgcctttttgattaaatattcta-acttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAAGTGGTTAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAA
                                                   ||   |  |  |    | ||||    ||  |    | ||  | || | || ||||||| |  | ||     | ||||   ||   ||    |   | |  ||||||| |   || |||||||| ||||||||||||||| | || |||||| |||||||||||| ||  ||||| ||||  || ||    ||||| ||||  || || ||||| ||||| |
--------------------------------------------------gtaagatggctagtcttttctat--tatggaggcaatgttgaaaagtgtataatttttgtatacaaa----gtataataccttccatta--ttaactaaccaaatattttgcgctgttgtagGTCCAGAATTTAATAGAACGCTGTCTACAGCTATATATGAATAGAGGAGAAGTTGTTAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTA

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaggatatatattctttgctaaacctttgactagttttctgttattgcctacttttacgtgcacatcctatatcgtgtggattgtattttatagggatgatttttggaagctaatctgatctaatctgttttttttgcctttttgattaaatattctaacttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAAGTGGTTAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAA
                |  |  | |  |||||     ||  ||| |||    ||| |||       |   |  ||||         ||| |   || |   || | | |   |    ||  |   || ||| |    ||   |  |||| ||   || | | |  |||||||||| ||||| ||||||||||| || ||||| || ||||| | |||||| || || || || ||  ||||||| |||| |||||| |||||||| ||||
---------------gtaagaaacaaatttgagctccttcttgtcatttttaactatta-aaaagtaggtttcatcgctctctccctatcta--agtgtaaatatgttgtgtcctccctcgt---atatgtgtaacatg---tgatgataaacacttttgaatgatgtagGTTCAAAATTTGATAGAAAGATGTCTTCAGTTGTACATGAACAGAGATGAGGTCGTGAAGACTCTCTTGACTCGTGCAAGGATAGACCCTGGATTTACAA

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g00990.t01 (Vitis vinifera), 3'ss of exon 3
gtaaggatatatattctttgctaaacctttgactagttttctgttattgcctacttttacgtgcacatcctatatcgtgtggattgtattttatagggatgatttttggaagctaatctgatctaatctgttttttttgcctttttgattaaatattctaa-----cttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAAGTGGTTAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAA
                                                |       |||  |||         || |  |   || | |||| | | | |||| |    |||   | || | | ||||||||| || || |    | | ||| | ||  ||      |  |  |||| |||||||| |||||| | ||||||||||| || ||||| |  ||||||||||| || || ||  ||| ||| |||| ||||||||||||||| ||||
------------------------------------------------gtaagacattatttgctttctactaatggatttttttttttttttttgtgttgatctccaaaagg-gagctcaacaaatctgtttcttatgtcgggcttaataatttttgcaaaaactttcctccagGTCCAGAATTTGATAGAACGGTGCCTACAGTTGTACATGAACAGGGATGAAGTGGTGAAGACCCTCTTGAGTCGTGCAAGGATAGATCCTGGATTTACAA

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|308222668|gb|HO760643.1|HO760643
EST:     CTGCTACAAGTAATGACAGCAAAAAAGTTTCACGGCAGGATATTGAGTTT                         GTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAA
genomic: CTGCTACAAGTAATGACAGCAAAAAAGTTTCACGGCAGGATATTGAGTTTgtaaggatat ... acttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAA
EST: gi|192295880|gb|FG990904.1|FG990904
EST:     CTGCTACAAGTAATGACAGCAAAAAAGTTTCACGGCAGGATATTGAATTT                         GTCCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAA
genomic: CTGCTACAAGTAATGACAGCAAAAAAGTTTCACGGCAGGATATTGAGTTTgtaaggatat ... acttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAA
EST: gi|302141431|gb|HO212307.1|HO212307
EST:     CGGCAGGATATTGAGTTT                         GTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAA
genomic: CGGCAGGATATTGAGTTTgtaaggatat ... acttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgatctaatctgttttttttgcctttttgattaaatattctaacttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAAGTGGTTAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAA
                                        ttctaac  putative branch site (score: 1)
                                              cttttgt  CT-rich tract
                          tttttgattaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatatatattctttgctaaacctttgactagttttctgttattgcctacttttacgtgcacatcctatatcgtgtggattgtattttatagggatgatttttggaagctaatctgatctaatctgttttttttgcctttttgattaaatattctaacttttgtagGTTCAGAATTTAATAGAAAGATGCCTACAGTTATATATGAATAAAGATGAAGTGGTTAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG