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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatattgtgagaatttgactggaatcttgaatgctgtttcaatttattgttctttagaactgttaagggtcttacttctttatgtttactgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT

Basic information

species Glycine max
transcript GLYMA05G30180.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30180.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g39790.4 (Oryza sativa), 3'ss of exon 2
---aaatattgtgagaatttgactggaatcttgaatgctgtttcaatttattgttctttagaactgttaagggtcttacttctttatgtttactgatttg-cagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT
   ||  |    |  || |  |      |  || ||  |  ||        | |    || | ||      |   | | ||||    ||||    |||   |||||| | ||||||||||| || || |||||||||||||| ||||||||||| ||||| || ||||||||||||||||| ||| | ||  ||||||||||||
atgaagaaacaaggaaagtatatcacttttctgtataattctttggcgccct-tatgctatatcttggcgtgacataatttctc---gtttgggaattaaacagGTTCGAGAGTATATTGATGATACAGAAGACTATGTCAATATTCAACTTGACAACCAGCGTAATGAACTTATTCAGCTTCAGCTTACACTGACTATTGCAT

upper sequence: GLYMA05G30180.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G453832_T01 (Zea mays), 3'ss of exon 3
-------aaatattgtgagaatttgactggaatcttgaatgctgtttcaatttat-tgttctttagaactgttaagggtcttacttctttatgtttactgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT
       |  | | ||||  |    | | |  | |||     |   |||||  || | ||| |  | | |||  | | |  |   || ||    |||        |||||| ||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| || |||||||| || || || ||| | ||  |||| |||||||
atttctgatttttggtgaagaaaccattcg--ttttggtgttttcatcaatccatctattcatctgga-tgtggatgctgatttgtccttgaaattaaaa-----cagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTTGACAACCAGCGTAATGAACTAATCCAACTCCAGCTTACACTGACCATTGCAT

upper sequence: GLYMA05G30180.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G145794_T01 (Zea mays), 3'ss of exon 3
aaatattgtgagaatttgac--tggaatcttgaat---gctgtttcaatttattgttctttagaact-gttaagggtcttacttctttatgtttactgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT
    |||       | ||     | |||| |  ||   | |||||  ||  |    ||| |  | || | || || | ||  ||  || |    | | |    |||||| ||||||||||||| ||||| |||||||| |||||||||||||| || ||||| || || ||||| ||||| || ||| | ||  | || |||||||
----atttctgatttctggtgaagaaatcattcattttggtgttttcatcaagccatctattcatctcgatatggatgttgatttcttcttgaaaataaa--acagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGACAACCAGCGTAACGAACTCATTCAACTCCAGCTTACACTTACGATTGCAT

upper sequence: GLYMA05G30180.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0034g02550.t01 (Vitis vinifera), 3'ss of exon 3
aaatattgtgagaatttgactggaatcttgaatgctgtttcaatttattgttctttagaactgttaag---ggtcttacttctttatgtttact------gatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT
      |    ||  |   ||||   ||||     | |  || || ||| | |||   ||   ||  |   | | |   ||  || | ||| ||      | |||| ||||| ||||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| ||||| || || ||||| ||||| |||||||
-----ctacaggagatgttctgg---cttggcaattatccca-ttcattttccttccaaataattgtgtttgatttctttttcttttttttcctatatgggttttgtagGTTCGGGAGTATATTGATGACACAGAAGACTATGTTAACATCCAACTGGACAACCAGCGAAACGAACTCATTCAACTCCAATTGACCTTGACCATTGCAT

upper sequence: GLYMA05G30180.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33726 (Selaginella moellendorffii), 3'ss of exon 3
aaatattgtgagaatttgactggaatcttgaatgctgtttcaatttattgttctttagaactgttaagggtcttacttct-ttatgtttactgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT
                                               |   |    || |  |||     ||||  |||| |||||  |     ||||||| |  |||||||||| || ||||||||||||||| ||||||| || || || |||||| | || ||  | || || || ||| |    ||||  ||||   
----------------------------------------------gtaagttgcaaggatcgttttctttcttctttctcttatgcctctc--tttgcagCTCCGGGAGTATATCGATGACACTGAAGACTATATCAACATCCAGCTCGACAACCACAGGAACGAGATGATCCAACTCCAGCTCGTTTTGATCATTGGCG

upper sequence: GLYMA05G30180.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37073 (Selaginella moellendorffii), 3'ss of exon 3
aaatattgtgagaatttgactggaatcttgaatgctgtttcaatttattgttctttagaactgttaagggtcttacttct-ttatgtttactgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT
                                               |   |    || |  |||     ||||  |||| |||||  |     | ||||| || |||||||||| || ||||||||||||||| ||||||| || || || |||||| | || ||  | || || || ||| |    ||||  ||||   
----------------------------------------------gtaagttgcaaggatagttttctttcttctttctcttatgcctctc--tctgcagCTTCGGGAGTATATCGATGACACTGAAGACTATATCAACATCCAGCTCGACAACCACAGGAACGAGATGATCCAACTCCAGCTCGTTTTGATCATTGGCG

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|11274996|gb|BF325320.1|BF325320
EST:     TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCT                         GTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
genomic: TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattc ... tgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
EST: gi|120493277|gb|EH221444.1|EH221444
EST:     TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCT                         GTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
genomic: TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattc ... tgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
EST: gi|120493204|gb|EH221371.1|EH221371
EST:     TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCT                         GTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
genomic: TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattc ... tgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
EST: gi|209719907|gb|BW665990.1|BW665990
EST:     TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCT                         GTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
genomic: TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattc ... tgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
EST: gi|120493425|gb|EH221592.1|EH221592
EST:     TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCT                         GTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
genomic: TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattc ... tgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
EST: gi|24206093|gb|BU965346.1|BU965346
EST:     TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCT                         GTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
genomic: TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattc ... tgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
EST: gi|51338037|gb|CO981903.1|CO981903
EST:     TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCT                         GTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT
genomic: TTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattc ... tgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgttctttagaactgttaagggtcttacttctttatgtttactgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT
                                          tactgat  putative branch site (score: 2)
                                  tttatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatattgtgagaatttgactggaatcttgaatgctgtttcaatttattgttctttagaactgttaagggtcttacttctttatgtttactgatttgcagGTTAGGGAGTATATTGACGACACTGAAGACTATGTCAACATTCAACTTGATAACCACCGAAATGAACTTATTCAGCTGCAGTTGACGTTGACTATTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - -ttgactg
- - - - - - - - - - - - - - -gaatgct