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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaattaatcatatactgcttaaaattaaggttttgttgcagaatctgtttgaattttactgatgttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC

Basic information

species Glycine max
transcript GLYMA07G33310.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G33310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G142507_T02 (Zea mays), 3'ss of exon 3
gtgaaattaatcatatactgcttaaaattaaggttttgttgcagaatctgtttgaattttactgatgttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC
|| |     || ||||||||  | |  | |   |  | || |   || | |||  |  ||| ||    ||  ||   || | |   | |||||||   |||||||| |||      ||  | |  || |||||  ||||||||||||| ||||||||||||||| |||||||||| || || || ||| |||| 
gtaatgaagat-atatactgggtcatgtgattttcctttttct--atttatttccaggttagtgtc--tgacttgcatgttctttgtctgttagGAAAGAATGTGCGTGCACAGGGGTTAGGTTCTTTGCTATCTTGTCAATGCAGAGGTCCGGGAGTGGATGGGTTGAGACGTTGTTGAATAGCCATCCTAAT

upper sequence: GLYMA07G33310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G877077_T01 (Zea mays), 3'ss of exon 2
gtgaaattaatcatatactgcttaaaattaaggttttgttgcagaatctgtttgaattttactgatgttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC-----
  | ||  ||  ||||||||  |     |  | |||||         |  |||  |  ||| |||      | |   || | |   | |||||||   |||||||| |||      ||  | |  || |||||  ||||||||||||| || |||||||||||| ||||||| || || || || ||| ||||      
--gtaacgaag-atatactgtgtc---ctctgattttg---------cctttttcaggttagtgactgacttgtgggtgttctttgtctgttaggaaagAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAATATTAG

upper sequence: GLYMA07G33310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G877077_T02 (Zea mays), 3'ss of exon 2
gtgaaattaatcatatactgcttaaaattaaggttttgttgcagaatctgtttgaattttactgatgttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC
  | ||  ||  ||||||||  |     |  | |||||         |  |||  |  ||| |||      | |   || | |   | |||||||   |||||||| |||      ||  | |  || |||||  ||||||||||||| || |||||||||||| ||||||| || || || || ||| |||| 
--gtaacgaag-atatactgtgtc---ctctgattttg---------cctttttcaggttagtgactgacttgtgggtgttctttgtctgttagGAAAGAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAAT

upper sequence: GLYMA07G33310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G34420.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaaattaatcatatactgcttaaaattaaggttttgttgcagaatctgtttgaattttactgat--gttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC
|| ||   |   | | |  | || |   |    |  ||||   || |||    |  || || ||||  ||   ||| |  | | ||  | | ||||||  |||||| |||||||||| ||  | || || || ||||| || ||||||||||| || ||||| ||||||||||| || ||||||| |||| |||||
gtaaagagagatacaaaaagtttgagccttta-tcatgtttt-gagtctaaaagc-ttgtattgattagtgcttttgtgggttttgaatgttttagGGATGAATGTTCTTGCCACCCGGTTAGGTACTTTGCGATTCTATCGATGCAGAGATCTGGTAGTGGCTGGTTTGAGACTTTGTTAAACAATCATACTAAC

upper sequence: GLYMA07G33310.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29778 (Selaginella moellendorffii), 3'ss of exon 1
gtgaaattaatcatatactgcttaaaattaaggttttgttgcagaatctgtttgaattttactgatgttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC
                   | |  | |   |   || |        |||   |   || ||   | | || |  |     | |   | |   |||  ||||||    |||   || || |  |  ||||   | || || |||||| ||||||| |||||||||||||||||| |  | ||||| ||| | |||
-------------------gttccaga---aatcttggaaaggatctctagctagtttctaacaaaggtggtcgaaac--tttttttcttccagGAAGGAATGCAGGTGCGTGCCAGTCCATTTCTTCGTCCTCCTCTCGATGCAGCGATCCGGCAGTGGATGGTTTGAGACGCTCCTCAACAGCCATCCAAAC

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|193356982|gb|FK319618.1|FK319618
EST:     CCTTGGGAGATTCCTTTTGTGCATTACCCTCACCCCCAAACTTACAGCAG                         GGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCA
genomic: CCTTGGGAGATTCCTTTTGTGCATTACCCTCACCCCAAAACTTACAGCAGgtgaaattaa ... cctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCA
EST: gi|193390546|gb|FK355010.1|FK355010
EST:     CCTTGGGAGATTCCTTTTGTGCATTACCCTCACCCCCAAACTTACAGCAG                         GGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCA
genomic: CCTTGGGAGATTCCTTTTGTGCATTACCCTCACCCCAAAACTTACAGCAGgtgaaattaa ... cctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagaatctgtttgaattttactgatgttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC
                    tactgat  putative branch site (score: 2)
                                             cctttgtt  putative PPT
           tttgaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaattaatcatatactgcttaaaattaaggttttgttgcagaatctgtttgaattttactgatgttgctttatttggtatgcctttgttagGGCGGAATGTGCTTGCCACCCTGTGCGCTATTTCGCTATTCTGTCAATGCAGAGATCCGGGAGTGGATGGTTTGAGACGTTTTTAAACAGTCATGCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA