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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacactttaagacatcattgactgataattgtactctttgggattttgttgtgtttatgcattctttatacatgttatctgatatgaaggactatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTATGCCAGTGGAACGCATTGGCTTTATGCTTATG

Basic information

species Glycine max
transcript GLYMA02G04360.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 11
cacactttaagacatcattgactgata-attgtactctttgggattttgttgtgtttatgcattctttatacatgttatctgatatgaaggactatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTATGCCAGTGGAACGCATTGGCTTTATGCTTATG
             ||  ||| ||  ||   || | ||| ||  | ||| ||  ||| | | | |    |||  |||| |    |||  |   |   | |||||| ||||||||  | || || || ||  |  |||| |||||||| || ||||||||||||||||| ||||| ||||| |||
-----------gtatacttg-ctactacgatgca-tctgtgtaactttcttcggttcacg-actgggaatat-tgttgttaactatacactgcatctgcagGTATGTGTTTGGGCTCACCCATATCCCAAGGCTGGAGGACTGGCCTGTCATGCCAGTGGAACGCATCGGCTTCATGCTCATG

upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
cacactttaagacatcattgactgataattgtactctttgggattttgttgtg--tttatgcattctttataca-tgttatctgata----tgaaggactatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTATGCCAGTGGAACGCATTGGCTTTATGCTTATG
        |  |    ||  |   ||| || |    |||    ||||| | ||  ||| || |||     ||   || | |||||||    ||  | |  ||  |||||| || |||||  | ||||||||||| ||  ||||||||||||| || ||||||||||| | |||||| |||| ||| |||
-------gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
















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|209703142|gb|BW664664.1|BW664664
EST:     ACTTGGGTTCAGAAGAATAGATCATTGGAAGAAGCCGATATAGTTCTTTG                         GTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTAT
genomic: ACTTGGGTTCAGAAGAATAGATCATTGGAAGAAGCCGATATAGTTCTTTGgttagtgcac ... actatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTAT
EST: gi|209702402|gb|BW656378.1|BW656378
EST:     ACTTGGGTTCAGAAGAATAGATCATTGGAAGAAGCCGATATAGTTCTTTG                         GTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTAT
genomic: ACTTGGGTTCAGAAGAATAGATCATTGGAAGAAGCCGATATAGTTCTTTGgttagtgcac ... actatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgtgtttatgcattctttatacatgttatctgatatgaaggactatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTATGCCAGTGGAACGCATTGGCTTTATGCTTATG
                               atctgat  putative branch site (score: 4)
                                              ctatttc  putative PPT
                   tttatacatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacactttaagacatcattgactgataattgtactctttgggattttgttgtgtttatgcattctttatacatgttatctgatatgaaggactatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTATGCCAGTGGAACGCATTGGCTTTATGCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatatg