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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

Basic information

species Glycine max
transcript GLYMA04G37050.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 21
agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatg---cagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
  ||  |||         ||   || | |    | || |   || |  | || | ||  | | ||  | |  |     |||| | |||| |    ||   ||||| || || || ||  || | ||||| || ||||| ||||| |||||||||||||| || || || ||||| || |||||||| |||||||| || || |
gttatgaatggatgggggtac--tacttttggatagtggaattttttatttccattttatttgatagtgaactgacttttgtta-ttgcttatgttgtgccagCCATGTAAAGGAATATTACTTTTTGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATAT

upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
--agtaaaaatcacaaacattaaag-taatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgc-agCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
  || || | ||  |    || | | |||  |     || |   |  || ||  |  |     | |    |||| ||||  || |  |||   ||| || | ||||||| || || ||  || | ||||| || ||||| || || |||||||||||||| ||||| || || || || |||||||| |||||||| ||||| |
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgt--ttat--attctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
-agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
   |     ||   || | |       |   ||  | | |   ||  | |     |||  |  | | || ||        | |   | | |||  |||||||| || || || || || |||||||| || |||||||| || ||||| ||||||||||| ||||| || |  ||||||| ||| || ||||||||||| |
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtcttt-atgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
-----agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttat-attgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
      |      ||| ||| ||| |  |  | | |   | |||   ||  | |     |||  |  | |  | || | | || |  || | |    || |  ||||| || || || || || |||||||| ||  ||||||| || ||||| ||||||||||||||||| || || ||||||||||| ||  |||||||||| |
aatttggctttcctca-aaaaatttatctcctataa---tttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtact--tctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT

upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
-agtaaaaatcacaaacattaaagtaatgtgaa-gttgtaggccttctcttgtca-aattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
 |||  |  |||     |  | || | |   ||   | |  ||  |   |  |   |||| |  ||      | | | | | ||| |||||       ||||||| |||||||| || ||  ||||||| |||||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||
cagttca--tcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgt-aattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT

upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
                                           ||| |       |||||  | |||||   ||||  |   |||||    |    |||||| || | |||  | || ||||||||||| || ||||| |||||||| |||||||| ||||| |||||||| || |||||||||||||||||||| ||||
------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtc-taacgaatttatatg---gcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
                                                |||    || ||||    ||| | |  |  |  | |     ||     |||||| || | |||  | || ||||||||||| || ||||| |||||||| |||||||| ||||| |||||||| || |||||||||||||||||||| ||||
---------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtc-taacgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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|16283953|gb|BI945829.1|BI945829
EST:     TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAG                         N
genomic: TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttacttta ... ttccatgcag-
EST: gi|16283953|gb|BI945829.1|BI945829
EST:     TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAG                         N
genomic: TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttacttta ... ttccatgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
                                        ttgccttcc  CT-rich tract
       aaattattatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
agtaaaaa
- - - - -cacaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattgtg