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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtctactaatcaatatatgttttttgactgtttgtcttcatgaaccattccctaagaatgttgttggctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCATTTACTGGTGATGTTGAAGCTGTTGATCCG

Basic information

species Glycine max
transcript GLYMA16G17190.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17190.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g47400.2 (Oryza sativa), 3'ss of exon 4
------------------------gtattgtctactaatcaatatatgttttttgactgtttgtcttcatgaaccattccctaagaatgttgttggctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCATTTACTGGTGATGTTGAAGCTGTTGATCCG
                           |  | || ||   ||   | |   |   |  |||    | | ||| | |||||       ||   |   | |  |||||||||||  |||||||||   |||||||| |||| |||||||||||||| || || || ||||| |||   || ||||| 
tatatgaatgtggacaatgctagaaagtcttataatatgaaacggagggagtagtatagttcacatgcttgatcgattcct-----gtgcaatcatcaaaaccagATTTCTACAATTGGAACAAGGTCAAGGTTCGGTACTGTGATGGGTCATCTTTCACCGGCGATGTGGAAAAAGTAGATCCT
















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|16346702|gb|BI972297.1|BI972297
EST:     ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAG                         ATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
genomic: ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAGgtattgtcta ... gctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
EST: gi|6567013|gb|AW234640.1|AW234640
EST:     ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAG                         ATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
genomic: ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAGgtattgtcta ... gctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
EST: gi|21675217|gb|BQ627568.1|BQ627568
EST:     ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAG                         ATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
genomic: ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAGgtattgtcta ... gctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
EST: gi|298194576|gb|HO043048.1|HO043048
EST:     ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAG                         ATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
genomic: ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAGgtattgtcta ... gctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
EST: gi|19935349|gb|BQ080379.1|BQ080379
EST:     ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAG                         ATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
genomic: ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAGgtattgtcta ... gctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
EST: gi|17519199|gb|BM188241.1|BM188241
EST:     ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAG                         ATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT
genomic: ATCACTTTCCTTTTCTGGGTTTTTCAGTAACAGTAAAAAGTTCAATCCAGgtattgtcta ... gctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgactgtttgtcttcatgaaccattccctaagaatgttgttggctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCATTTACTGGTGATGTTGAAGCTGTTGATCCG
 ttttgac  putative branch site (score: 3)
                                              ctattcc  putative PPT
                               taagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtctactaatcaatatatgttttttgactgtttgtcttcatgaaccattccctaagaatgttgttggctattccagATTTCTATGATTGGAACAGAATCAAGGTTAGGTATTGTGATGGGTCATCATTTACTGGTGATGTTGAAGCTGTTGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT