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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctttttcgcccgtgttattctgtcttggtgtattattttcccatgatcctatcttattgggcaactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC

Basic information

species Glycine max
transcript GLYMA04G39500.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 13
gtttgctttttcgcccgtgttattctgtcttggtgtattattttcccatgatcctatcttattgggcaactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
       |||    |     | ||||   |    ||  |   | |   || |  |   | |||  |      ||  |||| ||||| || |||||||| || |||||||||||||| ||||| ||||||||||||||  | ||| ||||  |  | || |||||||| || ||||||||||| 
------gtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattgattttgtt-taattcttttccagTGGGGAGTTTGTTGTGGTTAACAAGCATCTTCTCCATGATTTGACTGAAATGGGTGTTTGGACTCCAGCTCTGAAAAATAAGATAATTTATGAAGATGGT

upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 13
--------gtttgcttttt------cgcccg--tgttattctgtcttggtgtattattttcccatgatcctatcttat-tgggcaactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
         | ||||  ||      ||  |    ||| || ||  |   || ||| ||  |      |  |   |||  ||   |  |   | ||   ||||| || |||||||| || |||||||||||||| ||||| |||||||| |||||  | ||||| |||    | || || |||||| ||||||||||||| 
gtctgcaaatctgctccttgttaaacgttcaaccgttgttttggttacatgaatttttgccagtctgttttggtttacatgactagtttccttttggcagTGGCGAGTTTGTTGTAGTAAACAAGCATCTTCTCCATGATTTGACTGAGATGGGTATTTGGTCCCCTGTTCTGAAAAACAAGATTGTCTATGAAGATGGT

upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 13
gtttgctttttcgcccgtgttattctgtcttggtgtat-tatttt----cccatgatcctatcttattgggcaa-ctgtttgt-ttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
|| ||        | | |  || |   |    |||| |  |||||      ||||  | ||| | ||||  |   || ||| | ||| ||||| ||||||||||| || |||||||||||||||||||| ||||||||||||||  | ||| |||||||  | || ||  |||| || ||||| ||||| 
gtctgtaacaatactctt--tacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAATGGGCATTTGGACTCCTACTCTGAAAAACCAGATAATATATGATGATGGT

upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 13
------------gtttgctttttcgcccgtgttattctgtcttggtgtattattttcccatgatcctatcttattgggcaactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
              |  ||  |||    | ||  ||   |  || ||||  || | | ||||    ||   | |    | | | |||||| | ||||| ||||||||||| || ||||||||||||||||||||  |||||||||||||  | ||| ||||||| || || ||  |||| || || || || || 
gtctgtaacaatactccctacttctttagggtgtttacattgtgatgtac-atgtgcacatgtgattaatcttt----ctattttttgttcc-agTGGGGAATTTGTTGTGGTCAACAAGCATCTTCTTCATGATCTGACTGAAATGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGT

upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 13
gtttgctttttcgcccgtgttattctgtctt----ggtgtattattttc-ccatgatcctatcttattgggcaactgtttgtttct-agTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
||||| |||    |||       |   | ||    | | || || |||       |||  |   |  |       ||||| ||| | ||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||| || ||||| |||||  | |||||  |||| || |||||  |||||
gtttgttttgctaccctaacctgttcattttctaagatttagtacttttgttgccatctaagtctcctctttccttgtttctttgtcagTGGTGAATTTGTTGTGGTAAACAAGCATCTTCTTCATGACTTAACTGAGATGGGTCTTTGGTCACCTACTCTTAAGAACCAGATAATTTATGAGAATGGC

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|193356079|gb|FK322680.1|FK322680
EST:     GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGA
genomic: GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGA
EST: gi|193614757|gb|FK562795.1|FK562795
EST:     AGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
genomic: AGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
EST: gi|193517711|gb|FK475324.1|FK475324
EST:     GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTG
genomic: GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTG
EST: gi|31311230|gb|CD396433.1|CD396433
EST:     CGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
genomic: CGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
EST: gi|6963924|gb|AW432617.1|AW432617
EST:     GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
genomic: GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
EST: gi|208080492|gb|GD879004.1|GD879004
EST:     GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
genomic: GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
EST: gi|208137130|gb|GD934546.1|GD934546
EST:     GTGTTTTGAACCATATACTTCAAATAATACTACAGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
genomic: GTGTTTTGAACCATATACTTCAAAT-AT-CTACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
EST: gi|15199949|gb|BI424092.1|BI424092
EST:     GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
genomic: GAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggtgtattattttcccatgatcctatcttattgggcaactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
                                            tttgtttct  CT-rich tract
     tgtattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctttttcgcccgtgttattctgtcttggtgtattattttcccatgatcctatcttattgggcaactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG