Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgtatctctggtttttactgttctgttgatttgtgtctgacttaccaatctcttgatgcattctgagtaactattccttacttttgcattacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCATCCATACTCTATAATAGAGTGTGAGCCTAAGCGGGAAG

Basic information

species Glycine max
transcript GLYMA09G38530.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 5
----ttctgtatc-tctggtttttactgttctgttgatttgtgtctgacttaccaatctcttgatgcattctgagtaactattccttacttttgcattacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCATCCATACTCTATAATAGAGTGTGAGCCTAAGCGGGAAG
    || ||||   |    |||||| | | ||||  |||||    |||  || || |   |  ||  | | ||| |    |||  | | | ||  |||||| |||||||| ||||| || ||||| ||||||||||| || || ||| ||||||||||||| |||||||| ||||||||||| || ||||| ||||| || | ||
tgggttttgtacaattctatttttattttcctgtc-atttgctggtgaaataacatttatt--atatactttgatttgggatt--taattattttattactgcagGTTGTCTTCACCGGAGGTCGCACACAACCTGGCACAACAAAGTCTGATGAGGGGGAGCGCCATCCTTACTCTATAATTGATTGTGAACCTAATCGTGTAG
















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|26045706|gb|CA783207.1|CA783207
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAT
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|5687979|gb|AI940994.1|AI940994
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGATTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|209717990|gb|BW671821.1|BW671821
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|7284994|gb|AW597481.1|AW597481
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|27427457|gb|CA938977.1|CA938977
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|21286052|gb|BQ473923.1|BQ473923
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|16104801|gb|BI892541.1|BI892541
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|10709482|gb|BF009206.1|BF009206
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|13480362|gb|BG509705.1|BG509705
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|20449584|gb|BQ253708.1|BQ253708
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|120533835|gb|EH261968.1|EH261968
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|21677809|gb|BQ630160.1|BQ630160
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|6726947|gb|AW311227.1|AW311227
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|7042245|gb|AW472139.1|AW472139
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|120533411|gb|EH261544.1|EH261544
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|16347133|gb|BI972728.1|BI972728
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|6724745|gb|AW309144.1|AW309144
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|16347997|gb|BI973592.1|BI973592
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|16997181|gb|BM086553.1|BM086553
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
EST: gi|120533741|gb|EH261874.1|EH261874
EST:     TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAG                         GTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG
genomic: TTGAATCTTCAGACCTTAACTTTTCAAGATACGGCGATACCTTTTTTGAGgcaagcttcc ... attacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaatctcttgatgcattctgagtaactattccttacttttgcattacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCATCCATACTCTATAATAGAGTGTGAGCCTAAGCGGGAAG
                                tccttac  putative branch site (score: 2)
                                              ttacttc  putative PPT
                         taactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgtatctctggtttttactgttctgttgatttgtgtctgacttaccaatctcttgatgcattctgagtaactattccttacttttgcattacttcagGTTGTTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCATCCATACTCTATAATAGAGTGTGAGCCTAAGCGGGAAG

ttctgta
- - - - -tctggtt
- - - - - - - - - - - - tctgttg
- - - - - - - - - - - - - - - - - -gtgtctg
- - - - - - - - - - - - - - - - - - - - - -cttacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct