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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttattcaattatggatacctgatcgaattctgtcaaatctagtttggtcctgacttctatttttttctctccctcaaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA

Basic information

species Glycine max
transcript GLYMA10G34370.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G52180.1 (Arabidopsis thaliana), 3'ss of exon 4
--gtattttt-tattcaattatggatacctgatcgaattctgtcaaatctagtttggtcctgacttctatttttttctctccctcaaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA
| |||| ||| | | | | |||| || || | || | || |||| | | | | ||| | ||| | |||| ||||||||||| |||||| | |||| ||||||||| ||||| ||||||||||| ||||||||| ||||||| ||
gttcacttttatatccttctctcaaatgatgattttgttttgg-atatgtggtactttcctcgtgttcttactgtatgctctcctttattgctagACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGA

upper sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 5
gtattttttattcaattatggatacctgatcgaattctgtcaaatctagtttggtcctgacttctatttttttctctccctcaaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA
|| | ||| | | | | || || | || |||| | || | | |||||| | | ||| ||||| | ||| ||| |||||||| |||||| | || || ||||| |||||||| || ||||||||||||||||||||||| |||||
gtgataccatttctactctttaattaggagaagtttttttcctttctaagaagatcat----ttgatttttgtttttcctccaaatggc-agAGTCCAGAAGATGTTGACAAGCTTCGGAGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA
















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|120532166|gb|EH260299.1|EH260299
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
EST: gi|17022153|gb|BM093187.1|BM093187
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
EST: gi|193463792|gb|FK427016.1|FK427016
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGTGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
EST: gi|10845400|gb|BF068537.1|BF068537
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
EST: gi|24205361|gb|BU964614.1|BU964614
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
EST: gi|209709966|gb|BW681009.1|BW681009
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
EST: gi|6916528|gb|AW398058.1|AW398058
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGTGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
EST: gi|7589574|gb|AW705345.1|AW705345
EST:     TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG                         ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT
genomic: TGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAGgtatttttta ... aaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaaatctagtttggtcctgacttctatttttttctctccctcaaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA
                 tcctgac  putative branch site (score: 2)
 tcctgacttctatttt  CT-rich tract
 acttctattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttttattcaattatggatacctgatcgaattctgtcaaatctagtttggtcctgacttctatttttttctctccctcaaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG