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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctataggctccagtacattgtaccagcataaacaatattataatagagatttgcaaatgttaggaaatcgtttgattgtggtcatatatcacttatgcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAG

Basic information

species Glycine max
transcript GLYMA17G01960.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01960.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G840928_T01 (Zea mays), 3'ss of exon 7
-------------------------------------ctataggctccagtacattgtaccagcataaacaatattataa-tagagatttgcaaatgttaggaaatcgtttgattgtggtcatatatc--acttatgcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAG
                                     |  |||  ||   |   || ||  |   |     ||    | | ||    |||   | | | ||  |||   |   ||||  |||| | ||  |  | || ||| | |  |||||||   | |||||| || ||||| |||||||| |||||||| ||||||||||||||
gtatattagtaaattctaaaaaggctctgctcagatgccttagcttcacttttgttata--attttggcttattccctgactatcttttttttattttgagctaatacatatgttgttttcatgtttctgaaatctgaagTTACACAAGTGAGTACTTTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG

upper sequence: GLYMA17G01960.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0020g02800.t01 (Vitis vinifera), 3'ss of exon 7
ctataggctccagtacattgtaccagcataaacaat--attataatagagatttgcaaatgttaggaaatc-gtttgattgtggtcatatatcacttatgcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAG
   | ||| | |   || |  |  | || ||  ||     | |        ||||     |  | |||  |  | || || |  |  |  ||   || ||||||||| |||||  |  |||||||||||||  |||| ||||| ||||| |||||||| |||||||||||
--gttggc-ctatcccacttcatgaacaaaattaactggctttttctttcttttgtgggagccatgaaccccatctggttctaatactccatactttgtgcagTCAATTCAGTAGGCATCTATGGTTCTCCTCGACGCTGTGGCGGCCAGGGTGATATACTTTCTGGAAG

upper sequence: GLYMA17G01960.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S35_49V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------ctataggctccagtacattgtaccagcataaacaatat-tataatagagat----ttgcaaatgttaggaaatcgtttgattgtggtcatatatcacttat-gcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAG
                                                             ||   ||| || ||  || || |  |    | ||| | | ||  |||  |    |||    | |     | |       |     | | |  |||  | | |||||   |     |  |   ||||| |||||| ||||||||||||||||||||||| | |||||||| ||
gtgcgtacctctgacatatacctaaaccagtttgtacttattattagaaattaaattgtgatacgagcttca-taatttctatcctcgaccataatttctgtatcagacttctttttgtttttctcctagagtgaggcattctaatttagagttcatgtgttgcagTTTTAAGTTCGGATTATTATGGCTCTCCCCGACGTTGTGGTGGCCAAGGTGATGTGCTTTCTGGCAG

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|5752521|gb|AI959808.1|AI959808
EST:     TACTATCCTAAGCAAAGGAAATTCTGATCTCATAAGCGATGGTGACACAG                         TCAAATCAGTGAGTGTCTATG
genomic: TACTATCCTAAGCAAAGGAAATTCTGATCTCATAAGCGATGGTGACACAGgcaggtcttt ... acttatgcagTCAAATCAGTGAGTGTCTATG
EST: gi|22524066|gb|BU082877.1|BU082877
EST:     TACTATCCTAAGCAAAGGAAATTCTGATCTCATAAGCGATGGTGACACAG                         TCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTG
genomic: TACTATCCTAAGCAAAGGAAATTCTGATCTCATAAGCGATGGTGACACAGgcaggtcttt ... acttatgcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTG
EST: gi|192319733|gb|FK011871.1|FK011871
EST:     TACTATCCTAAGCAAAGGAAATTCTGATCTCATAAGCGATGGTGACACAG                         TCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTG
genomic: TACTATCCTAAGCAAAGGAAATTCTGATCTCATAAGCGATGGTGACACAGgcaggtcttt ... acttatgcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatttgcaaatgttaggaaatcgtttgattgtggtcatatatcacttatgcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAG
                        gtttgat  putative branch site (score: 5)
         aaatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctataggctccagtacattgtaccagcataaacaatattataatagagatttgcaaatgttaggaaatcgtttgattgtggtcatatatcacttatgcagTCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG