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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcccatgaaattggatggtactcatcgtagcttatactctgctgtgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG

Basic information

species Glycine max
transcript GLYMA10G03740.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G03740.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g06740.1 (Oryza sativa), 3'ss of exon 6
tgcccatgaaattggatggtactca-tcgtagcttatactctgctgtgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG
       | | ||   || |  ||| |   |  ||||    |  ||  | ||  |  | ||| |  | |    ||||| ||  ||    |  |||    |||||||| || ||||| || || || |||||||| || |||||||||||||||||||| || |||
catttcagtatttcactgtttatcagttaaattttatttggttttggttattgttgttccattggatgctccttgattgtga-attgcacaaatttgacagAGCTGTACCATCTGCCGTTTTCTCCCAACCACCCATCGGACAAGTTGGTCTTACTGAAGAGCAG

upper sequence: GLYMA10G03740.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G172322_T02 (Zea mays), 3'ss of exon 6
-----tgcccatgaaattggatggtactcatcgtagcttatactctgctg-tgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG
     || | ||    |  ||   |   ||| |   | |    | |   | | |      || | |   |    | | ||  |   ||| | |  |    |    ||||| | ||||||||||| || || ||||||||||| ||||||||||||||||||||||| |||
gattgtgtctatcccgtccgacactggccatggggccatgctatttatggatatcaactcaactgaccactcttccattg--tgaattacaatttttggca----gAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG

upper sequence: GLYMA10G03740.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
tgcccatgaaattggatggtactcatcgtagcttatactctgctgtgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG
  |  |  |    |  |  |||   |   || ||| |   |     | |    |   ||        | | |||| |   || | |       |    |||||||| || |||||||| ||||| || ||||| ||||||||||||||||||||||| ||||||
ccctgagaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtttgatctgtattagctacctgactagattgtttcttcttatgagcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG

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|192299302|gb|FG988702.1|FG988702
EST:     GCATTAGTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAG                         AGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
genomic: GCATTAGTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAGgtattatata ... cattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
EST: gi|15286301|gb|BI470192.1|BI470192
EST:     GTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAG                         AGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
genomic: GTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAGgtattatata ... cattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
EST: gi|11273725|gb|BF324101.1|BF324101
EST:     GCATTAGTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAG                         AGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
genomic: GCATTAGTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAGgtattatata ... cattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
EST: gi|19347352|gb|BM892232.1|BM892232
EST:     GCATTAGTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAG                         AGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
genomic: GCATTAGTAAAAACACTGTTTCAGGATAACCCAACAAAACCTGATTATAGgtattatata ... cattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
EST: gi|16347393|gb|BI972988.1|BI972988
EST:     GTTTCAGGATAACCCAACAAAACCTGATTATAG                         AGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT
genomic: GTTTCAGGATAACCCAACAAAACCTGATTATAGgtattatata ... cattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG
                        aactgat  putative branch site (score: 3)
                                        ttcctcatt  putative PPT
        taattcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcccatgaaattggatggtactcatcgtagcttatactctgctgtgttttagtaattcatagcctcccaactgattctgttatattcctcattatctagAGCTGTTCCTTCTGCTGTATTTTCTCAACCACCAATTGGACAAGTTGGTCTTACTGAGGAACAG

- -ccatgaa
- - - - - - tggatgg
- - - - - - - - - - - - - - - - - - -ctctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg