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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTTGGCTACCATTCCTATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcctttcacttatgtgcctctttgtttttcttacaagtgacttatttaacggtttaattttgattttggcttacag

Basic information

species Glycine max
transcript GLYMA01G42950.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 5'ss of exon 2
CCACTTGGCTACCATTCCTATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcctttcacttatgt--gcctctttgttt-ttcttacaagt-gacttatttaacggttta-attttgattttggcttacag------------
 ||| |||| ||||| || ||||| || || ||||| |||||||| ||||| ||||| ||||| || || |||||| | | |||||| ||||||||||||||   | |   |||||| |      || |||| |   | |||||| || ||  ||| ||    | || || |  || |     || |             
TCACCTGGCCACCATCCCCATCACCGGCACCGGCATCAACCCAGCGAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGGCCATGCCTGGGATGACCATgtgagtttaaattcactgaaaccaacccctttctccctccttacatgtagaaatatatatatatatatatatatatatatatatatatatatatatatat

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
CCACTTGGCTACCATTCCTATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcctttcacttatgtgcctctttgtttttcttacaagtgacttatttaacggtttaattttgattttggcttacag-------------
 ||  |||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| || || || || || |||||| |||| ||||| ||||||||| |||  || |  |  | |          ||  |  |  ||| |  | | |  | |  | | |  |  | |||||||     |   |             
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGAC-ATG-

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 3
CCACTTGGCTACCATTCCTATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcctttc-----------------acttatgtgcctctttgtttttcttacaagtgacttatttaacggtttaa-ttttgattttggcttacag--------------
 |||||||| ||||| || |||||||||||||||||||||||||| ||||||||||| |||||||| || | |||| |||| ||||| |||||||||   |||  |||  |                    || || |    | |   |  || | |    | | ||   |  | ||| || || | ||| || |||                  
TCACTTGGCCACCATCCCCATCACAGGAACTGGCATTAACCCAGCCAGGAGTCTTGGAGCTGCTATCATCTTCAACAGAGAGCATGCATGGGATGACATGgtaggtgttttgatgagaaaaaaaaaaaaaaacctaaggaattttgcatcctt-tgatggttaaattgagtttcagttcaagttcttattgtgactttttttctcttgctttcag

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S102_107V6.1 (Physcomitrella patens), 5'ss of exon 3
CCACTTGGCTACCATTCCTATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAAC---CGAGACCATGCTTGGGATGACCATgta-----tatgtcctttcacttatgtgcctctttgtttttcttacaagt---gacttatt---taacggtttaattttgat---tttggcttacag--------------------------------------------------------------------
    ||||| |||||||| ||||| ||||||||||||||||| ||  | ||||| || || || |  || ||||||   |   || |||| ||||  || || ||       ||   ||| |||   |    ||     ||     |  | ||   |||||||    |   | |||| |||  ||   || ||  || |                                                                     
---TTTGGCCACCATTCCCATCACCGGAACTGGCATTAACCCTGCACGTAGTCTGGGCGCGGCCACCATCTACAACACGCAGCACAATGCCTGGGCCGATCACgtgagttgcattctcttccaccactcctgctgaaaattcaaggttaaggttaggacttatcgtctggagatttattttctatgggttcggtctagaaacgaatggttatcaggcacaatatgaaggagctgtaacctctctgaaatgttgattgtgctgctgcag

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|37996387|gb|CF807976.1|CF807976
EST:     GAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
genomic: GAGACCATGCTTGGGATGACCATgtatatgtcc ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
EST: gi|192305304|gb|FG997556.1|FG997556
EST:     GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCAT                         TGGATTTTTTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcc ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
EST: gi|193601187|gb|FK553048.1|FK553048
EST:     ATACAACCGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
genomic: ATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcc ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
EST: gi|193385708|gb|FK350286.1|FK350286
EST:     GCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
genomic: GCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcc ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
EST: gi|193418094|gb|FK381730.1|FK381730
EST:     GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcc ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
EST: gi|192295284|gb|FG985938.1|FG985938
EST:     GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcc ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
EST: gi|31474331|gb|CD416359.1|CD416359
EST:     GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCAT                         TGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT
genomic: GTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcc ... tggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACTTGGCTACCATTCCTATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcctttcacttatgtgcctctttgtttttcttacaagtgacttatttaacggtttaattttgattttggcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT