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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatcaatatgtcatgcattgatcccacaatggctagttacattgtgttattcaaataaaaaagtttgtgttttgttaaatatttgtatgttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA

Basic information

species Glycine max
transcript GLYMA10G09280.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G09280.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027378_T02 (Zea mays), 3'ss of exon 1
ttatcaatatgtcatgcattgat--cccacaatggctagtta-cattgtgttattcaaataaaaaagtttgtgt-tttgttaaatatttgtatgttaaa--tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA
       ||  || ||  ||  |  |  | ||     | |||  |  ||  || |  |||  |     ||   |  |||   ||       ||||||||  |||||||||| | ||||||||  |  | |||||||| || |||||||| || || ||||| ||||| ||||| ||||||||||||||||||| ||||||||| ||
------gtagttcctgtttttgtaacatataagattcatttagtagagtactagtagaattcattgcattacctgcttgcgtaactgacaaatgttaaaaatgcagTTCCTCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATCTA

upper sequence: GLYMA10G09280.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
ttatcaatatgtcatgcattgatcccacaatggctagtta-cattgtgttattcaaataaaaaagtttgtgt-tttgttaaatatttgtatgttaaa--tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA
   | | | |    |   |  |    | |||    | |||  |  ||  || |  |||  |     ||   |  ||||  ||       ||| ||||  |||||||||  | ||||||||  |  | |||||||| || |||||||| || || ||||| ||||| ||||| |||||||||||||||||||  |||||||| ||
---ttagt-tcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA

upper sequence: GLYMA10G09280.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g02580.t01 (Vitis vinifera), 3'ss of exon 1
ttatcaatatgtcatgcattgatcccacaatggc--tagttacattgtgttattcaaataaaaaagtttgtgttttgttaaatatttgtatgttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA
|  ||   |  | |  | |||||     |   ||  || | | |   | ||||| || |   ||  |||| |   | |||| | | || || ||  ||||||| ||| | |||||||||||||| ||||| ||||||||||||||||| || ||||||||||| || || |||||||||||||||||||| |||||||||||
tggtctgaagcttagcctttgatatttaaggcgccttattcagacaattttatt-aattttcaagatttgcgcacttttaagtctctgcat-ttccatgcagTCCCTCGAAACTTCAGATTGCTTGAGGAACTTGAACGTGGAGAAAAGGGTATTGGAGATGGTACTGTCAGCTATGGAATGGATGATGGAGATGACATTTA

upper sequence: GLYMA10G09280.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
ttatcaatatgtcatgcattgatcccacaatggctagttacattgtgttattcaaataaaaaagt--ttgtgttttgttaaatatt-tgtatgttaaa--tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA
     || |  ||||  | || |  ||   | ||||||   ||  ||   ||  | |          || || | | |||| | || | |||||| ||   | |||||||||||||||  |  | || || || |||||  | ||||| ||||| ||||| |||||||| || |||||||| ||||| |||||||||||| | | 
----gaagagttcatagaatgttgacatg-tagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT

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|38192514|gb|CF921720.1|CF921720
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|27808883|gb|CB063305.1|CB063305
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCATATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|6069578|gb|AW099241.1|AW099241
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTTAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|207841754|gb|GD813638.1|GD813638
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|4314038|gb|AI461157.1|AI461157
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|10233465|gb|BE802353.1|BE802353
EST:     ATCCAGTGTCGTGG                         TTCCTAGGAACTTGAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: ATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|209724423|gb|BW662954.1|BW662954
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGCGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|13563351|gb|BG551571.1|BG551571
EST:     CCTACGCATCCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCACATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|208206857|gb|GE002550.1|GE002550
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGTGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
EST: gi|38193817|gb|CF923023.1|CF923023
EST:     CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGG                         TTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA
genomic: CCTACGCAACCCATCCATGACGCTTGGCTTAGGAGGATCCAGTGTCGTGGgtcagtgtcc ... ttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattcaaataaaaaagtttgtgttttgttaaatatttgtatgttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA
        aaataaaaaagtttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatcaatatgtcatgcattgatcccacaatggctagttacattgtgttattcaaataaaaaagtttgtgttttgttaaatatttgtatgttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG