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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaggagtggttgcctgaactgcattagtttgtttagttacacattatttatacattattttacttgcgcattaatttgttttactatttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAACGAGGCTGATGTGGAGTCTATGATTAAAACT

Basic information

species Glycine max
transcript GLYMA18G01280.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 3
agaaaggagtggt-tgcctgaactgcattagtttgtttagttacacattat--ttatacattattttacttgcgcattaatttgttttactatttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAACGAGGCTGATGTGGAGTCTATGATTAAAACT
   |  || || | |  | |   |||||  ||||    | ||      | |  || | | |||  |   | |   |  |   ||   |     |   ||  ||||||| |  ||||||||||| ||  |||| ||  | |||||||||||||| || || |||||||| |||||||||||| | 
---attgaatgttgtttccggggtgcatgtgttttgaaaattttgttctgttgttctgccttaaatagatggaagaagatactgaggtttccgtattttacagATTGAAGGATTTGGTGGTCAGGCAATTACCTTCCGAGGAGATGTTTCTAATGAAGCCGATGTGGATTCTATGATTAAAGCA

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G043602_T03 (Zea mays), 3'ss of exon 2
agaaaggagtggttgcctgaactgcattagtttgtttagttacacattat-ttatacattattttacttgcgcattaatttgttttactatttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAACGAGGCTGATGTGGAGTCTATGATTAAAACT
  | |    || ||   ||    |||  | ||| |     ||    ||     | ||  ||||  ||||   ||   | |  | || | || |  ||  ||||||| |  | ||| || || ||  |||| ||||| ||||||||||| || ||||||||||| || |||||||| |||   
gaacacacatgtttttttggggagcagaactttttcagtctaatttttgcaccaaactatattgaacttaaacacgtaatattatttccatatt-ttacagATTGAAGCATCTGGAGGCCAGGCCATTACCTTTGGAGGAGATGTTTCCAAAGAGGCTGATGTTGAATCTATGATAAAAGTG

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g01840.t01 (Vitis vinifera), 3'ss of exon 3
agaaaggagtggttgcctgaactgcattagtttgtttagttacacattatttatacattattttacttgcgcatt---aatttgttttactatttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAACGAGGCTGATGTGGAGTCTATGATTAAAACT
  |    | |  |  | |   |    ||  |  |         |  ||| ||  || |  |   || |    |||   |||   |   | ||||| ||||||||||||||| |||||||| ||||||||||| ||||| || |||||||| || ||||  ||||| || || ||||||||||| 
--attataatcatgtcatattcaatgtttttaaggcagtcagaatgttacttg-acttattaagacctcaaaattgtgaatacttacaattatttgcttgtagATTGAGGAATTTGGTGGGCAAGCTCTTACTTTTGGGGGTGATGTTTCCAAGGAGGAAGATGTAGAATCAATGATTAAAACC

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0010g02670.t01 (Vitis vinifera), 3'ss of exon 3
-agaaaggagtggttgcctgaactgcattagtt-tgtttagttacacattatttatacattattttacttgcgcattaatttgttttactatttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAACGAGGCTGATGTGGAGTCTATGATTAAAACT
   |    | |  ||      | |     |||  |||||||    ||   | ||  | | ||    || |      |||||| ||  ||| |||| ||  |||| ||||  | ||||||||| ||| |||| ||||| ||||| ||||| || ||||||||||||||  | ||||||||| ||
gttatttcatttcttatggttatttaggcagtgatgtttaggc-tactcaaattgcaaaataaaaaacattattgataatttattcaactctttcttt-cagATCGAGGCATGTGGTGGTCATGCTATTACTTTTGGAGGAGACGTTTCAAAAGAGGCTGATGTGGAAGCAATGATTAAAGCT

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|58017082|gb|CX703824.1|CX703824
EST:     TATGCAAGGTCATCCAAGGAAGCTGAGGAGTTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTACC
genomic: TATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
EST: gi|213600146|gb|DB964310.1|DB964310
EST:     TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
EST: gi|298177236|gb|HO023483.1|HO023483
EST:     TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGA
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGA
EST: gi|7042369|gb|AW472263.1|AW472263
EST:     TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
EST: gi|22540327|gb|BU090170.1|BU090170
EST:     GTCAACTATGCAAGGTCATCCAAGGAAGCTGGAG-ANGGTT-CCAAGGAG                         ATCGAGGAGTTT
genomic: GTCAACTATGCAAGGTCATCCAAGGAAGCTG-AGGA-GGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTT
EST: gi|192334676|gb|FK025223.1|FK025223
EST:     TGGTCAACTATGTAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
EST: gi|192296853|gb|FG990229.1|FG990229
EST:     TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC
EST: gi|298187125|gb|HO034274.1|HO034274
EST:     TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATG
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATG
EST: gi|19345915|gb|BM890795.1|BM890795
EST:     TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAAGAGGTTTCCAAGGAG                         ATTGAAGAGTTTGGTGGT
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGT
EST: gi|192333774|gb|FK025497.1|FK025497
EST:     TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAG                         ATTGAGGAGTTTGGTGGTCAAGCCCTTACATTTGGTGGAGATGTTTCTAAC
genomic: TGGTCAACTATGCAAGGTCATCCAAGGAAGCTGAGGAGGTTTCCAAGGAGgtaaaatttg ... ttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttatacattattttacttgcgcattaatttgttttactatttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAACGAGGCTGATGTGGAGTCTATGATTAAAACT
                          cattaat  putative branch site (score: 3)
                                    ttttactatttcctt  putative PPT
                           attaatttgttttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaggagtggttgcctgaactgcattagtttgtttagttacacattatttatacattattttacttgcgcattaatttgttttactatttccttgtagATTGAGGAGTTTGGTGGTCAAGCTCTTACATTTGGTGGAGATGTTTCTAACGAGGCTGATGTGGAGTCTATGATTAAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - -ggagtgg
- - - - - - -tgcctga
- - - - - - - - - - - tgcatta