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

...ttgtagtagtgaatgttttccagttcttgagaaatttttagaacagtctgcttcattgtttaccagtcaacctctcattttatcttttatattattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGCCTATTGTTAGTCTAAG

Basic information

species Glycine max
transcript GLYMA11G37040.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37040.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g29690.1 (Oryza sativa), 3'ss of exon 2
ttgta-gtagtgaatgttttccagttcttgagaaatttttagaacagtctgcttcattgtttaccag-tcaacctctcattttatcttttatattattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGCCTATTGTTAGTCTAAG
  ||| ||| |     |  | ||    |        |||||||    | |   | || |   |  |  ||||  | |||| ||    |   | |   |  ||| ||||   | ||||||||| ||||||||||||||||||||||||| || |||||||| ||  ||||
--gtatgtaatttgc-tccttcaacagtgactgtccttttagattgatataaatgataggaaataatctcaaagtttcatgttcctatccctgtc--tatagGTGACATGCTTGGTGGCCACGTTGATGACATGGAAGCAGATTGGAGTAAACCTATTGTAAGCATAAG

upper sequence: GLYMA11G37040.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G844096_T02 (Zea mays), 3'ss of exon 4
------------------ttgtagtagtgaatgttt-------tccagttcttgagaaatttttagaacagtctgcttcat--tgtttaccagtcaacctctcattttatct-tttatattattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGCCTATTGTTAGTCTAAG
                  ||    ||||||| | ||       | || || || |||  | | | ||  ||     |||||  |  ||  |  |      || |  |  |    ||| |||  |  ||| ||||   | ||||||||  ||||||||||||||||||||||||  || |||||||| ||  ||||
gtatgtatagtatgtccgttaagatagtgaaggcttagattgatacatttttttagagttatcttgatgagctgtattcatgctccttctcgtttctgtactgaaatactaagcttagattgatgtagGTGACATGCTTGGTGGCCATGTTGATGACATGGAAGCAGATTGGACAAAACCTATTGTAAGCATAAG

upper sequence: GLYMA11G37040.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0010g03650.t01 (Vitis vinifera), 3'ss of exon 4
ttgtagtagtgaatgttttccagttcttgagaaatttttagaacagtctgcttcattgtttaccagtc--aacctctcattttatcttttata--ttattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGCCTATTGTTAGTCTAAG
 || | |  | |  | |||  |    ||  |     |  ||    |   |  |||||  |||    |   | |  ||  ||||  |||| ||   |  || |||| || |   | || |||||||| ||||||||||||||||||||||  || ||||| || ||  | ||
-tgcactgataa--gctttgtaaccttttggtgggatggaggtttgag-gtatcattaattatggatttaagcaactggttttcactttcattgttcttttcagGTGATATGCTTGGGGGCCACCTAGATGACATGGAAGCAGATTGGACTAAACCTATAGTGAGCATGAG

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|298172230|gb|HO021822.1|HO021822
EST:     TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAG                         GGGACACATCGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC
genomic: TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAGgtatgctcaa ... attattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC
EST: gi|6071440|gb|AW100827.1|AW100827
EST:     TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAG                         GGGACACATTGNGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC
genomic: TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAGgtatgctcaa ... attattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC
EST: gi|192299837|gb|FG990074.1|FG990074
EST:     TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAG                         GG-ACACATTGG-TGGCCACCTTGATGACATGGA-GCAGAT
genomic: TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAGgtatgctcaa ... attattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGAT
EST: gi|209717977|gb|BW671806.1|BW671806
EST:     TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAG                         GGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC
genomic: TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAGgtatgctcaa ... attattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC
EST: gi|209712172|gb|BW681378.1|BW681378
EST:     TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAG                         GGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC
genomic: TGGTGTTGAGTTCAGACCTGATGCTGCAATAGTGAATTACTTCGGCCTAGgtatgctcaa ... attattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgcttcattgtttaccagtcaacctctcattttatcttttatattattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGCCTATTGTTAGTCTAAG
                                              ttattcc  CT-rich tract
                           tctcattttatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtagtagtgaatgttttccagttcttgagaaatttttagaacagtctgcttcattgtttaccagtcaacctctcattttatcttttatattattccagGGGACACATTGGGTGGCCACCTTGATGACATGGAAGCAGATTGGAGCAAGCCTATTGTTAGTCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - -tgaatgt
- - - - - - - - - - - gttcttg
- - - - - - - - - - - - - - - - - - - - - - - -ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccagtca