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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tacttaagaattttattgtcagaaggaacatttcagcattcttttgatcttatgaatttgttgtgaacatttgtatcctgttttcaaaacttcataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG

Basic information

species Glycine max
transcript GLYMA18G10030.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------tacttaagaattttattgtcagaagga------acatttcagcattcttttgatcttatgaatttgttgtgaacatttgtatcctgttttcaaaactt-cataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG
                                                                                 |||||||| |  |||| |||  |  |      ||| || ||   |  |   ||  | ||   | | ||     | |  | |  | |   |||  |||    |  |  || || | |||||||| || ||||| |||||||| ||||| || || || || ||||||||||| || |||| ||| |||||||||||||| |||||||| || | 
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaaga-tgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG-

upper sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 5
-------------------------------------tacttaagaattttattgtcagaaggaacatttcagcattcttttgatcttatgaatttgttgtgaacat-ttgtatcctgtttt---caaaacttcataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG
                                     | |    |  |||||     ||   | | |  |  |   | | |  |    | |||     | |  |  | || ||    |||||   || |  |    | ||  || || | ||||||||  |||| ||||| ||||| || || || || ||||||||||||||||| || |||| ||| ||||| |||||||| |||||||| || | 
gtgcgtgtaggattcattagaaattctttattgattctgcaatggtgttttaagagaagttaggaaacgttggg--tgtctcaaatagaagaaccaaatatatagttgttttagatagttttgaccatatgtattcacctcttgcagATTGTGACAAGCCTAGCTGACCCATCTGCGAACATAATTTTCGGTGCCGTTGTTGATGACCGTTACACTGGTGAGATACATGTGACAATCATTGCGACAG-

upper sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 5
tacttaagaattttattgtcagaaggaacatttcagcattcttttgatcttatgaatttgttgtgaacatttgtatcctgttttcaaaacttcataac-tgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG
       | |   |||| |      |      || || || |||  ||    ||  | |    || |   |  |    | || |||    ||       |  || |||| ||||||||||| || ||||| || ||||| || |||||||| || ||||| |||||||||||||  || ||||||||||| || || || || || | 
-------gtacggtatttttgtcttggtttactcggctttgtttcaat----tgggtatacactgtattataatgcagtcttctcatgttttgggggggttttgcagGTCGTGACAAGTTTGGCAGACCCATCGGCCAACATCATATTTGGAGCTGTTGTGGATGATCGCTACACCGGAGAGATTCATGTAACGATAATCGCCACAG-

upper sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
tacttaagaattttattgtcagaaggaacatttcagcattcttttgatcttatgaatttgttgtgaacatttgtatcctgtt-ttcaaaacttcataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG
   |   |  |||| ||| ||      |  |   |   | ||||||      ||  ||| |  || |  ||  ||| ||  | ||   |  | ||| | |     |||| || |||||| | ||||| ||||| || || || |||||||| || ||||| || || ||||||||||||||||||||||||||||| |||||||| | 
--atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttt-tcttgcattttcttatgctaatatttgcatatccatgatt----cagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG-

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|193481514|gb|FK446437.1|FK446437
EST:     TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTT
genomic: TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTT
EST: gi|6846019|gb|AW348309.1|AW348309
EST:     TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
genomic: TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
EST: gi|6913484|gb|AW395014.1|AW395014
EST:     TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
genomic: TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
EST: gi|193567226|gb|FK523353.1|FK523353
EST:     GGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
genomic: GGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
EST: gi|193543186|gb|FK503695.1|FK503695
EST:     GGGGGGAGGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
genomic: GGGGGGA-GAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
EST: gi|298189601|gb|HO038004.1|HO038004
EST:     TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
genomic: TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
EST: gi|193554215|gb|FK513400.1|FK513400
EST:     GGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
genomic: GGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
EST: gi|31475903|gb|CD417931.1|CD417931
EST:     TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGG                         TGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG
genomic: TACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaa ... ctgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatttgttgtgaacatttgtatcctgttttcaaaacttcataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG
                                       tcataac  putative branch site (score: 2)
                            ttttcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttaagaattttattgtcagaaggaacatttcagcattcttttgatcttatgaatttgttgtgaacatttgtatcctgttttcaaaacttcataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT