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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaaatatacaagttcatcagctatcttgcatgatggtttcttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

Basic information

species Glycine max
transcript GLYMA10G42940.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 10
--gtaatgaaa-tatacaagtt----catcagctatcttgcatgatggtt--tcttaa-cactgaatg--------attatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
  |   || |  | ||| | ||     || | |||   ||     || ||  |||||| || | |||         ||| |  | |    | ||  ||||||||||| || |||||||||||||| || || || || || || || ||||||||||| |||||||||||| |||| ||||||
ttgcgttggatctttaccatttatgttattacctaatgtgtgctttgtttagtcttaaacaataaatatgtttaacattgtgctgtttcatcctaaacagATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G094497_T03 (Zea mays), 3'ss of exon 1
----gtaatgaaat-at-acaagttcatcagctatcttgcat-gatggtttcttaacactga------atgatta-tattttgaacttctgt----acagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
     |  ||   | || |    || | || |||| |    | | |||    |||| |||        |||  || |||| | | || |       |||||||| || |||||||||||||| || || ||||| || |||||||| ||||||||||| || ||||||||  |||| ||||||
tagcatgttggtctcatgatttatttaccatctatttcattttgttgggcatttaatactagtataccatgtctaatattgtaatctacccctaaaacagATATCACACACCCAACTCCTGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
gtaatgaaatatacaagttcatcagctatcttgca---------tgatggtttcttaacactga------atgatta-tattttgaacttctgt----acagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
 |||| ||| | |     || |  | | ||  | |         || |||    ||||| |         |||  || |||| | | || ||      |||||||| || ||||||||||| || || || ||||| || |||||||| ||||||||||| || ||||||||  |||| ||||||
-taataaaacaca-gctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 10
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 10
gtaatgaaatatacaagttcatcagctatcttgca-tgatggtttcttaacactgaatgattatattt--tgaactt---ctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
||||||  |   |  | | ||| |   |||| |   |||   ||||| |  |  |    | || | |   ||||| |    |  |||||||| || || || ||||| ||||| || || |||||||||||||| ||||| ||||| ||||| |||||  | ||| |||||
gtaatgtcaagcatca-tccat-attgatctagtggtgagaatttctcattatagtggcactacactcactgaacctgattttcacagATATAACACATCCCACTCCCGATCTCACGGGTTATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 10
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------gtaatgaaatatacaagttcatcagctatcttgcatgatggtttcttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
                                                                                       |  |  | |        || ||  || |   | |       || |    ||| |         || ||   ||  || |||||||||| ||||||| ||||||||| ||||||||||| || || || || || ||  | ||  ||||| |  | || ||||||
gtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgt---ggacttctccttgtctgtactaagcttcacctttgtggcatttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG

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|19452473|gb|BM953883.1|BM953883
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|16283344|gb|BI945501.1|BI945501
EST:     CTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: CTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|16283207|gb|BI945427.1|BI945427
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|16279679|gb|BI943560.1|BI943560
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|16278507|gb|BI942940.1|BI942940
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAAGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgcatgatggtttcttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
                tcttaac  putative branch site (score: 2)
                                            cttctgt  putative PPT
                           aatgattatattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaaatatacaagttcatcagctatcttgcatgatggtttcttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG