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

gtaagtggcttaccatgctaacttgatttcaattgattgatccttaaaatatgataaatgactatgtattatgtttgtgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGGTGCAACCTCGAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT

Basic information

species Glycine max
transcript GLYMA05G02740.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------gtaagtggcttaccatgctaacttgatttcaa--ttgattgatccttaaaatatgataaatgactatgtattatgtttgtgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGGTGCAACCTCGAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT
                        |  |  | || | |    |   |  |||     ||  |   | ||    ||  |     ||||| | |||||  | |       | || ||||||||||| |||||||||||  ||||||||||||| |||||||| || ||||| || || ||||| ||||||||||||||  | ||||| ||| | |||
gtgagtgatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcagCCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGGTGCGACTTCAAGGGAAAGTATCAAAGCTGTTCTCAAGCTACCTCGCCTT
















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|208243789|gb|GE040714.1|GE040714
EST:     ATGGAAAGGGTACTTGGTACATTACCACAGACCATGATGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAA-GGGTAGATTAGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGAgtaagtggct ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
EST: gi|208133298|gb|GD926555.1|GD926555
EST:     ATGGAAAGGGTACTTGGTACATTACCACAGACCATGATGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGAgtaagtggct ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
EST: gi|254324743|gb|GR834168.1|GR834168
EST:     CCATGATGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
genomic: CCATGATGAAGAGAGTCGAgtaagtggct ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
EST: gi|254323902|gb|GR840435.1|GR840435
EST:     ATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGAgtaagtggct ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
EST: gi|207792096|gb|GD766550.1|GD766550
EST:     ATGGAAAGGGTACTTGGTACATTACCACAGACCATGATGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGAgtaagtggct ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
EST: gi|58016463|gb|CX703205.1|CX703205
EST:     ATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGAgtaagtggct ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatccttaaaatatgataaatgactatgtattatgtttgtgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGGTGCAACCTCGAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT
 gattgat  putative branch site (score: 4)
        ttaaaatatgataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggcttaccatgctaacttgatttcaattgattgatccttaaaatatgataaatgactatgtattatgtttgtgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTAGACTGGCCTGAGGGTGCAACCTCGAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC