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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgatcaaagcacctatctctatgatctcatgtcattgcctgtgccagatcttgcaagttgtgaaaacctgagtgatattggacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCAGCAACAAAAGAGGAG

Basic information

species Glycine max
transcript GLYMA14G38800.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G28630.1 (Arabidopsis thaliana), 3'ss of exon 1
---gtaagttgat--caaagcacct--atctctatgatct-catgtcattgcctgtgccagatcttgcaagttgtgaaaacctgagtgatattg-gacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCAGCAACAAAAGAGGAG----------------------------------
     |  || ||  |||| |   |  ||   ||| |  | |||         |   | |||     ||     | ||        ||  |||  | ||||| || |||||||| ||||||||||| ||||||||||||||    || ||||||||| |||| |||                                  
ttttcattttaatatcaaatcgatttaatggttataacttgcatacttaaagataaactagactaatcatagcctcaattgactcctggaattatggcagGTGCTCTTCAATGACACAATATTTCACAACATTCACTATGGAAACCTTTCAGCAACAGAAGAAGAGGTGTACGATGCAGCTAGGCGAGCAGTGATTCACG

upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g08350.t01 (Vitis vinifera), 3'ss of exon 17
gtaagttgatcaaagca-------cctatctctatgatctcatgtc-att--------------gcctgtgccagatcttgcaagttgt------gaaaacctgagtgatat-------tggacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCAGCAACAAAAGAGGAG
||||||| || ||||||        || | ||| | || |    || |||              |||  ||    | |||||||| |||      || ||    ||  |          | |||||||||||||||||||||||||||| || |||||||| |||||||| || |||||||| || ||||||
gtaagtttatgaaagcaacaaacttctgtttctctaattttccttctattctgtaaattaataggcccttgtagtaccttgcaagctgttgtagtgataaggaaagcaactcctgcttgtcgacagGTACTTTTCAATGATACAATATTCCACAACATTCAGTATGGTCGTCTTTCAGCAACCAACGAGGAG

upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ24035 (Selaginella moellendorffii), 3'ss of exon 13
gtaagttgatcaaagcacctatctctatgatctcatgtcattgcctgtgccagatcttgcaagttgtgaaaacctgagtgatattggacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCAGCAACAAAAGAGGAG
                           ||| ||  |  |  |  ||       || |  |   || || |    |  |   | |    ||||| |||||||||||||| || ||  | |||||||| ||||||||||||||||||||  | || |||
--------------------------gtgaactgttccc--taactaatttgcatttcac---ttatgga---tttggcattgtacctcagGTTCTTTTCAATGATACTATCTTCTACAACATTCAGTATGGTCGGCTATCAGCAACTGAGGAAGAG

upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ24600 (Selaginella moellendorffii), 3'ss of exon 13
gtaagttgatcaaagcacctatctctatgatctcatgtcattgcctgtgccagatcttgcaagttgtgaaaacctgagtgatattggacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCAGCAACAAAAGAGGAG
                           ||| ||  |  |  |  ||       || |  |   || || |    |  |     |    ||||| |||||||||||||| || ||  | |||||||| ||||||||||||||||||||  | || |||
--------------------------gtgaactgttccc--taactaatttgcatttcac---ttatgga---tttggcatcgtccctcagGTTCTTTTCAATGATACTATCTTCTACAACATTCAGTATGGTCGGCTATCAGCAACTGAGGAAGAG

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|23734500|gb|BU765482.1|BU765482
EST:     TAACCCTTGAGAGTTTGCGGAAGTCCATTGGTGTTGTTCCACAAGATACT                         GTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCA
genomic: TAACCCTTGAGAGTTTGCGGAAGTCCATTGGTGTTGTTCCACAAGATACTgtaagttgat ... tattggacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcattgcctgtgccagatcttgcaagttgtgaaaacctgagtgatattggacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCAGCAACAAAAGAGGAG
                                          tgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgatcaaagcacctatctctatgatctcatgtcattgcctgtgccagatcttgcaagttgtgaaaacctgagtgatattggacagGTACTTTTCAATGATACAATATTTCATAACATTCACTATGGTCGGCTATCAGCAACAAAAGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG