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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttcttttaaacctcttcattttatgtcaggttagtatttatttgcttgcatgatgaaatatttgtcagcaatctgtcattgagtattatcatttgtcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG

Basic information

species Glycine max
transcript GLYMA20G38960.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g05660.1 (Oryza sativa), 3'ss of exon 4
--gtattttcttttaaacctcttcattttatgtcaggttagtatttatttgcttgcatgatgaaatatttgtcagcaatctgtcattgagtattatcatttgtcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG
    | |     |||  | |   ||||  |   ||| |||   | | ||   ||  |||       |   | |   || ||| || |||| || | | | | |  |   ||||| ||| || | || || || ||   ||| ||  ||||||||||||||||  |||| |||||||||||||| ||||| ||
gtagactgatgcttattcatggacattgcaaa-cagtttaacctatcttatgttttatgccatgccaaaagac--taaactgacagtgagcat-accttatatttta--cagGCTTGGTTGTTGTTTCTGTATACAACTTTAGCTCTGCGAGAGAACATATTACGAGTTAATGGAAGTGATATCCGTCCTTG

upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G154328_T01 (Zea mays), 3'ss of exon 4
gtattttcttttaaacctcttcattttatgtcaggttagtatttatttgcttgcatgatgaaatatttgtca-gcaatctgtcattgagtattatcatttgtcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG
|||   |||    ||    | |   ||  | |     || |||  ||   ||  || ||    |   ||||| || |   | || ||| |||    | ||  | |    |||| ||| |  ||||||| || ||| |||| || ||||| ||||||||| || |||| |||||||||||||||||||| ||
gtacactct----aatgcttgc---ttgcggcgatgcagcattagttgaatta-atcatatgtttcatgtcatgccaaaagacactga-tatctcaaattaccttgtatagGCTTGGTTATTATTCCTGTATACCAGTTTAGCTTTGCGTGAGAACATACTGCGAGTTAATGGAAGTGATATTCGTCCTTG

upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 3'ss of exon 4
gtattttcttttaaacctcttcattttatgtcaggttagtatttatttgcttgcatgatgaaat-atttgtcagcaatctgtc---attgagtattatcatttgtcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG
                                    ||     |||| | |  |   |   ||| || |||    ||   ||    ||||| | ||     ||  | |   ||||| |||||| | ||||||||||| ||||| || |||||||||||||| || ||||| |||||||||||||||||||| ||
-----------------------------------gtatcccctattagatctcgcaacccaattatgtgttcaaaactcgtgtgaattgaatgttgagtgtttgctttggcagGCATGGCTGTTGTTCCTTTACACAGGTTTAGCTTTGCGAGAGAACATCTTAAGAGTGAATGGAAGTGATATTCGTCCATG

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|14259702|gb|BG882610.1|BG882610
EST:     CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAG                         GCCTGGCTGCTA
genomic: CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAGgtattttctt ... tcatcatcagGCCTGGCTGCTA
EST: gi|298182431|gb|HO026606.1|HO026606
EST:     CTTGGGTTTGGTCTAGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAG                         GCCTGGCTGCTATTCCTTTACACC
genomic: CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAGgtattttctt ... tcatcatcagGCCTGGCTGCTATTCCTTTACACC
EST: gi|213590375|gb|DB963896.1|DB963896
EST:     CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAG                         GCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
genomic: CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAGgtattttctt ... tcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
EST: gi|192319099|gb|FK010635.1|FK010635
EST:     CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAG                         GCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
genomic: CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAGgtattttctt ... tcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
EST: gi|192320395|gb|FK012253.1|FK012253
EST:     CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAG                         GCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
genomic: CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAGgtattttctt ... tcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
EST: gi|209701984|gb|BW664584.1|BW664584
EST:     CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAG                         GCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
genomic: CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAGgtattttctt ... tcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
EST: gi|213594582|gb|DB958001.1|DB958001
EST:     CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAG                         GCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG
genomic: CTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGTACCAGgtattttctt ... tcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgaaatatttgtcagcaatctgtcattgagtattatcatttgtcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG
                                 tattatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttcttttaaacctcttcattttatgtcaggttagtatttatttgcttgcatgatgaaatatttgtcagcaatctgtcattgagtattatcatttgtcatcatcagGCCTGGCTGCTATTCCTTTACACCGGTTTGGCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG