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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataatatgctaaatctgagtccatcttcattgagaactaatgtaagtttttctatttggagctcttttgtttgattggttaacttgaggcaatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG

Basic information

species Glycine max
transcript GLYMA19G30580.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 20
---------------------------------tataatatgctaaatctgagtccatcttca--ttgagaac--taatgtaagtttttctatttggagctcttttgtttgattggttaacttgaggcaatgtg-----cagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG
                                 | |    ||||| |  ||    |||  | |  |||   |    ||  |||   |   |    | |||| ||  ||||||| | | || ||   |  || |      ||||| ||||| || ||||||||||| || ||||| || |||||||||||||||||||||| || |||||||  ||| || | | ||| ||| || |     |
gtgcgtttcccttctgtttacttgggttcaatatgttcattgctacagatgcacacatacttaggttgtatatggcaaactaaaaatggtttggagaagctattcagtttgat-gttcaattttgtgtcatatttttttcagGTTTGTGCTCCGTCATGTCATGATTGCTCCACATTACGTGCTTGGTGGGAAGAAGATGGAGGAAGAAGAAGCCGTTTCTACCAGACTGTAATTGGTAGTG

upper sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 10
-------------------------------------tataatatgctaaatctgagtccatcttcattgagaactaatgtaagtttttctatttggagctcttttgtttgat--tggttaacttgaggcaatgtg-cagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG
                                     | |   |   |||     ||  | |  | ||||| || |          ||   |   |  ||| | ||| |||||    || |   |      ||||  ||||| ||||| || |||||||||||||| || || || ||||||||||||||||||||||||| |||||||   || || | ||||| |||  | |     |
gtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaa-tggcacggagattcaga---gaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG

upper sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 21
lower sequence: AT2G40840.1 (Arabidopsis thaliana), 3'ss of exon 20
------tataatatgctaaatctgagtccatcttcattgagaactaatgtaagtttttctatttggagctcttt----------tgtttgattggttaacttgaggcaatgtgc---------agGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG
      |||  |     | |  |  |||  |||| | | | | ||       |||  | |  |  ||  | | |          || || | ||  ||| |  |   |  ||           |||| ||||| |||||||| || ||||| || ||| |||| |||||||||||||| || ||||| |||||||  | ||  |||||| | ||||| |     |
gttagatatttttcctcagacttctgtctttctt-acttatagcttcctaccgttcattttctgagaattttgtaatgggtgagtgattcactgcataattcaaactatcgtcttaatattttagGTGTGTGCTCCTTCATGCCACGACTGCTCTACCCTGCGAGCTTGGTGGGAAGAGGACGAAGAGAGAAGACAGCAGTACTTCAAGGAAGTGATTGGTGTAG

upper sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 19
tataatatgctaaatctgagtccatcttcattgagaact-aatgtaagtttttctatttggagctcttttgtttgattggttaacttgaggcaatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG
    |  |  |  || |  ||   |||    ||   | | |||       |  |   |   |    |||||||  || || |||||  |  | || | ||||| ||||| || ||||| ||||||||||||||| ||||||||||||||||||||||||||||||||||||  || ||||| |||| |||| | | ||| |
gggtaggttttccatttttgtttttctctcctggttattgaatccttacatcacatgtcacaatagttttgttgaataggctaactgaataccattt-cagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG

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|6725673|gb|AW310072.1|AW310072
EST:     GGTATTCCTTTTAAGTACAGCTACATGCCG                         GTATGTGCCCTTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAN
genomic: GGTATTCCTTCTAAGTACAGCTACATGACGgtaaggtttc ... caatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAA
EST: gi|18732935|gb|BM527331.1|BM527331
EST:     ATGAACCTGATCTGGAATTTGGTATTCCTTCTAAGTACAGCTACATGACG                         GTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAA
genomic: ATGAACCTGATCTGGAATTTGGTATTCCTTCTAAGTACAGCTACATGACGgtaaggtttc ... caatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttctatttggagctcttttgtttgattggttaacttgaggcaatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG
                                ggttaac  putative branch site (score: 3)
     ttctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataatatgctaaatctgagtccatcttcattgagaactaatgtaagtttttctatttggagctcttttgtttgattggttaacttgaggcaatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - -tatgcta
- - - - - - - - - - - catcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg