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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG

Basic information

species Glycine max
transcript GLYMA0028S00210.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatc-ttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
        |||  | |      | || |   | | ||| | | ||      || |  ||     ||          ||| | |  || | |||  || |||||| | |||||||||||||||||||| || || ||||||||||| || |  ||||| ||||| || |||||||| ||||| ||||| |||||  ||| ||
--------gtttgaacgcaagcaactatcgatagaacagtttaag------aaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG

upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
         ||| |  |  | |||  ||   | | ||| | | ||     |  || |||      || | | |   | |||    ||  |||   | |||||| | ||||||||||||||||||||||| || || |||||||| || |  ||||| || || ||||||||||| || || ||||| |||||  | | ||
-------gtttgaacttaagcaattactg-atagaacaatctgagagaagatgtaattt------gacttactttttcaatgc--tgaattt---aacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG

upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
        ||       ||  || | | |||||||    || |  |  ||   ||| |    | | || |  |||    | || |||| |||    | ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||   ||| || ||||| ||||| ||| | |||||  | ||||
--------gtaaagcagtgagaaccgc-atgttgcttgatactcattttt---tacat--gtgttaatgctctgctaatacatattgtattt----ttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG

upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
||| |        |  |||   |  | || | | ||   | |  ||  || | ||| |  |  ||||||||     |    |||||     |||  ||||||| |||| |||||||||||  |||||||||| ||||| ||||| || |||||||| || | ||| || ||||| || || ||  | |||||| ||| ||
gtaaaatgcaaaaactttgtctacatttacgct-cattgtttatgttgtttagtacgtgcaa-atgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG

upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
-----gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaa-atactttaaggatgattcagtgcc-ttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
     | || | |||   |||      ||   |   |||  |||| | | || |     ||   | || ||| | || |||  |   ||| |||||||      |||||  | || ||||||||||| ||||||||||| ||||| ||||| |||| |||||| || | |||||| ||||| ||||| ||  | |||||||| | ||
tactaggatgtgagtc-catcacatgcatacatgctttgt-cattttaaatcgtccgcgtaacattag-atggtccaatgctatctgtattttgtgttca----cagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG

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|151393898|gb|EV263769.1|EV263769
EST:     TAGTAGGTACTGCAGTTGCGAAGCTTCTTCCTGGACAGCCACGTGTTGAG                         AAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTACATT
genomic: TAGTAGGTACTGCAGTTGCGAAGCTTCTTCCTGGACAGCCACGTGTTGAGgtaaactgtt ... ttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
                             ccttaat  putative branch site (score: 4)
     aaatactttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - tgcacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgtg