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

...tcatttgtgatcacgtgcctttggatttttaatgttgcctattgttttttccttcatcttcttcatgaaaagcatctcacattgtgttttggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTTGTGCTCTTGATTTCCGCATGGATGAATGGGGAGTTGATGTGGCAATAAC

Basic information

species Glycine max
transcript GLYMA18G14740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G14740.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 2
--------tcatttgtgatcacgtgccttt--------ggatttttaatgttg----cctattgttttttccttcatcttcttcatgaaaagcatctcacattgtgttttggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTTGTGCTCTTGATTTCCGCATGGATGAATGGGGAGTTGATGTGGCAATAAC
        ||||||   |   |    |||         |||   || |  ||      || |  ||||   ||      |  ||||    | | |      |||| ||  | |   ||||||   ||||| |||||||| ||| || |||||||||| ||||| || || ||||| ||||||||||| ||||||||||||||||| ||||||||  ||||
gtaagaattcattttctaggccacatcttcatctgcaaggaaacttcacattaggattctgtcattttccactattgggttctcatttttaacgttcttttttgtatt--gaaatatcagATGAGTACCGTCATCCAGCACTCTTTCTTGTTGATGGGGTGTCATCCATATGTGCCCTTGATTTCCGTATGGATGAATGGGGAGTGGATGTGGCGTTAAC
















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|5607077|gb|AI901175.1|AI901175
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|19347288|gb|BM892168.1|BM892168
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|8669960|gb|BE191067.1|BE191067
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCA                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|120531737|gb|EH259870.1|EH259870
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|192312355|gb|FK005359.1|FK005359
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|192312356|gb|FK005360.1|FK005360
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|6134794|gb|AW133187.1|AW133187
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|5607145|gb|AI901243.1|AI901243
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|9259656|gb|BE347803.1|BE347803
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|120533482|gb|EH261615.1|EH261615
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|13562627|gb|BG550847.1|BG550847
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|120532136|gb|EH260269.1|EH260269
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATCGGAGTGTCTTCTATT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGAT-GGAGTGTCTTCTATT
EST: gi|11412210|gb|BF424221.1|BF424221
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
EST: gi|19452389|gb|BM953799.1|BM953799
EST:     GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCG                         ATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT
genomic: GACTGCAACTGGGGTCACCAATGACTTGGCCAAAGTGAGACAAATTCTCGgtgagtatgt ... ggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccttcatcttcttcatgaaaagcatctcacattgtgttttggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTTGTGCTCTTGATTTCCGCATGGATGAATGGGGAGTTGATGTGGCAATAAC
                            atctcac  putative branch site (score: 3)
                   atgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttgtgatcacgtgcctttggatttttaatgttgcctattgttttttccttcatcttcttcatgaaaagcatctcacattgtgttttggacactcagATTCCTACCGGCATCCAGCCCTCCTTATTGTTGATGGAGTGTCTTCTATTTGTGCTCTTGATTTCCGCATGGATGAATGGGGAGTTGATGTGGCAATAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - -cacgtgc
- - - - - - - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcacat