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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatacataaccggttggacagatttgtagccaatttgcacctcaacctgattgtaatcactaagagtatccttgtgcttctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAGCAGAAGGAATTGCCCAATGTGTCAAGCTCCTGTGGTGGAGGTGATACGT

Basic information

species Glycine max
transcript GLYMA12G08770.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08770.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g39690.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------gtaatatacataaccggttggacagatttgtagccaatttgcacctcaacctgattgtaatcactaagagtatccttgtgcttctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAGCAGAAGGAATTGCCCAATGTGTCAAGCTCCTGTGGTGGAGGTGATACGT
                                                     ||  |   |  |  | ||   ||||   |   |    ||||    |   |||  ||||      |  | || |   ||   |||| |  ||||||||| ||  |||| |||||||||||||| || ||||||||| ||| |||| || |||| |||||  |||| |  || ||  |  | |||||||| || 
gtttgaactcatgcttttcttctgaaataatgaataataggtccatgtagtttgttcttctctaatacagtataacagtactaatgatggtttgt---tttgcctctttgttgggggttggggtgt---tgactttctat--cagATGTGGGCACATGTGCACATGTTCAAAATGCGCGAATGAGTTGGTTCGAAGCGGAGGGAAATGCCCGCTGTGCCGTGCACCCATAATTGAGGTGATCCGA
















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|58017761|gb|CX704503.1|CX704503
EST:     GGACTTTGCTGTATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAG                         ATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAG
genomic: GGACTTTGCTGTATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAGgtaatataca ... tctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAG
EST: gi|8286387|gb|BE023946.1|BE023946
EST:     GGACTTTGCTGCATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAG                         ATGTGGTCATTTGTGTACATGTTCAAAATGTGCGAATGAGTTGCTTCAAAG
genomic: GGACTTTGCTGTATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAGgtaatataca ... tctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAG
EST: gi|58014309|gb|CX701051.1|CX701051
EST:     GGACTTTGCTGTATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAG                         ATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAG
genomic: GGACTTTGCTGTATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAGgtaatataca ... tctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAG
EST: gi|51335007|gb|CO978873.1|CO978873
EST:     GGACTTTGCTGTATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAG                         ATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAG
genomic: GGACTTTGCTGTATATGCTGTGAAAGCAATATCGATTCTTTGTTGTACAGgtaatataca ... tctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcacctcaacctgattgtaatcactaagagtatccttgtgcttctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAGCAGAAGGAATTGCCCAATGTGTCAAGCTCCTGTGGTGGAGGTGATACGT
           acctgat  putative branch site (score: 4)
                                           cttctgtt  putative PPT
                attgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatacataaccggttggacagatttgtagccaatttgcacctcaacctgattgtaatcactaagagtatccttgtgcttctgttgcagATGTGGTCATTTGTGTACATGTTCAAAATGTGCCAATGAGTTGCTTCAAAGCAGAAGGAATTGCCCAATGTGTCAAGCTCCTGTGGTGGAGGTGATACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG