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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgtgttcactttgtagatgtattataatattatttagaggtaggcttggatattttagatgcaagcatgtatataatttcattgtttttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGCTGGTTTTAT

Basic information

species Glycine max
transcript GLYMA05G36530.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 3'ss of exon 25
--tgttgtgttcactttgtagatgtattataatattat--ttagaggtaggcttggatattttagatgcaagcatgtatataatttcattgtttttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGCTGGTTTTAT
   ||||  ||    || | |     |  |  |   ||  || || ||   | | |||| |  | ||  |      |   |||||  | | || || || |||||| | ||| || ||||||||||| |||||||| || || ||||| |||||||||||||||
ttagttggattaggctttttggcagttggtgttcccatgctttgatgtcttcattgatactc-aaatctatcttcat---taattatagttttatttcttgcagTTAAATTTGACAGCAGGAGAAGAGGTTGAGATCGATTATGAAGTTGATGGCTGGTTTTAT
















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|51335525|gb|CO979391.1|CO979391
EST:     CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAA                         TTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGC
genomic: CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAAgtaagttgat ... ttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGC
EST: gi|7924509|gb|AW830535.1|AW830535
EST:     CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAA                         TTGAGTTTAACCGCAGGAGAGGAAGTTGAGATTGAGTACGAAGTAGAATGG
genomic: CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAAgtaagttgat ... ttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGA-TGG
EST: gi|151398994|gb|EV268865.1|EV268865
EST:     CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAA                         TTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGC
genomic: CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAAgtaagttgat ... ttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGC
EST: gi|16344465|gb|BI970060.1|BI970060
EST:     CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAA                         TTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGC
genomic: CTCAACATGGAAGTGCACTTTATGACTTCACAGCAGGAGGAGACGATGAAgtaagttgat ... ttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttggatattttagatgcaagcatgtatataatttcattgtttttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGCTGGTTTTAT
                                  tttcattgtttttcct  CT-rich tract
                        atgtatataatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgtgttcactttgtagatgtattataatattatttagaggtaggcttggatattttagatgcaagcatgtatataatttcattgtttttcctggcagTTGAGTTTAACCGCAGGAGAAGAAGTTGAGATTGAGTACGAAGTAGATGGCTGGTTTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- -tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - gcttgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgta