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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttattttttcatatagacaaatacatgcgttcatatagttgcacactaatgaatgtgtcctgtattgtggtaaattctgctggatcaattcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTAAAACCTATTCTTGATGAG

Basic information

species Glycine max
transcript GLYMA04G36770.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 18
--gtttattttttcatatagacaaatacatgcgttcatata-gttgcacacta---atgaatgtgtcct-gtattgtggtaaattctgctggatcaattcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTAAAACCTATTCTTGATGAG
   | |  |  |  ||   |   |||| | |  | | |||   |||   |||    ||||| |  |    || |  || ||   ||| || |        |    |||| || || ||||||||||||||||||||||||||||| ||||| ||||| ||||| || |||||||||
ccatgtggtacta-atggtgttgaatagaagtctccctatgcattgtgtactctctatgaacgcattaaagtgtgttgatatggtctccttgga------actgcagGAGCTACGAAAGGATGGTTTTGATCTTGCTGAAGCTCGATACAGAGAGCTTAAACCAATCCTTGATGAG
















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|9903008|gb|BE611976.1|BE611976
EST:     ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA                         GAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA
genomic: ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAAgtaggttttc ... ttcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA
EST: gi|193480934|gb|FK444373.1|FK444373
EST:     ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA                         GAACTCCGCAAGG
genomic: ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAAgtaggttttc ... ttcatcatagGAACTCCGCAAGG
EST: gi|11688791|gb|BF596467.1|BF596467
EST:     ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA                         GAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA
genomic: ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAAgtaggttttc ... ttcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA
EST: gi|21286225|gb|BQ474096.1|BQ474096
EST:     ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA                         GAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA
genomic: ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAAgtaggttttc ... ttcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA
EST: gi|26048263|gb|CA784790.1|CA784790
EST:     ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA                         GAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA
genomic: ATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAAgtaggttttc ... ttcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactaatgaatgtgtcctgtattgtggtaaattctgctggatcaattcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTAAAACCTATTCTTGATGAG
 cactaat  putative branch site (score: 2)
                           taaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttattttttcatatagacaaatacatgcgttcatatagttgcacactaatgaatgtgtcctgtattgtggtaaattctgctggatcaattcatcatagGAACTCCGCAAGGATGGTTTTGATCTTGCTGAAGCTCGGTACAGGGAGCTAAAACCTATTCTTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - -tacatgc
- - - - - - - - - - - - - - - - - - - - - -cacacta
- - - - - - - - - - - - - - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggta