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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatcctggtcttagtcataaataccttgctgtatgttaagattatttatttagtagctgttttctaatgatgtaagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA

Basic information

species Glycine max
transcript GLYMA16G07350.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g08060.1 (Oryza sativa), 3'ss of exon 1
gtataatcctggtcttagtcataaataccttgctgtatgttaagattatttatttagtagctg-ttttctaatgatgtaagttgtgaaatt--tttgttg----acagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
      |  || |     | || | || |||| | |  ||||   || |||  ||   | |||     ||  ||| | ||||| |    ||  ||||||     ||||||||||||||| || || |||||||| |||||| | ||||| ||||| ||||||||||| || |||||| |||||||||| || |||||||| |||||||
-----gtattgtttcatatgatca-tatcttg-tatg-gttatctttgtttggttgccaactgaccccctgctgaggaaagttattgttttcctttgttctgttacagATGGATGCCACCACTCCCAAGTACTCCAAGGCCCGTTATGATGAAATCGTGAAGGAAGTCTCATCCTACCTGAAGAAGGTCGGCTACAACCCTGACAAGA

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g08010.1 (Oryza sativa), 3'ss of exon 1
gtataatcctggtcttagtcataaataccttgctgtatgttaa-gattatttatttagtagctgttttctaatgatg-taagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
   | ||  |||| ||  | |||  |  | | |  | |||      | || |||||    |||| |  ||     || |  ||| |    | ||   | ||||||||||||||| || || |||||||| |||||| | || || ||||| ||||||||||| || |||||| |||||||||| || |||||||| |||||||
--cttata-tggtgtttataatatgtttcataccatttgtagttagtaatgtatttgtatgctggtgcctgcccctgatttgttttcctttgttctgttacagATGGATGCCACCACTCCCAAGTACTCCAAGGCCCGTTACGATGAAATCGTGAAGGAAGTCTCATCCTACCTGAAGAAGGTCGGCTACAACCCTGACAAGA

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g08020.1 (Oryza sativa), 3'ss of exon 1
gtataatcctggtcttagtcataaataccttgctgtatgttaagattatttatttagtagctg-ttttctaatgatgtaagttgtgaaatt-------tttgttg----acagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
           || | |       ||| |||| | |  ||||   || |||  ||   | | |     ||  ||| | ||||| |  | ||       ||||||     ||||||||||||||| || || |||||||| |||||| | || || ||||| ||||||||||| || |||||| |||||||||| || |||||||| |||||||
-----------gtttcatatgatcatatcttg-tatg-gttatctttgtttggttgccaaccgaccccctgctgaggaaagttattgatttgttttcctttgttctgttacagATGGATGCCACCACTCCCAAGTACTCCAAGGCCCGTTACGATGAAATCGTGAAGGAAGTCTCATCCTACCTGAAGAAGGTCGGCTACAACCCTGACAAGA

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g08050.1 (Oryza sativa), 3'ss of exon 1
gtataatcctggtcttagtcataaataccttgctgtatgttaagattatttatttagtagctgttttctaatgatg-----taagttgtgaaatttttgttg--acagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
      | || || ||| |  |   |   |      ||||  || ||| |||| | ||   ||||| ||| |         ||| | ||    || ||  ||  ||||||||||||||| || || |||||||| |||||| | ||||| ||||| ||||||||||| || |||||| |||||||||| || ||||| || |||||||
------tgctagtattaattttttttgtttcatatcatgtatag-ttagttatct-gtgtttgtttgctagtccctgcccctaattcgtttgcttatttctgttacagATGGATGCCACCACTCCCAAGTACTCCAAGGCCCGTTATGATGAAATCGTGAAGGAAGTCTCATCCTACCTGAAGAAGGTCGGCTACAATCCTGACAAGA

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G343543_T05 (Zea mays), 3'ss of exon 2
-gtataatcctggtcttagtcataaataccttgctgtatgttaa-gattatttatttagtagctgttttctaatgatgtaagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
    | ||  |||| ||   |||   |||  |  || ||| |   | |||  |   || |  |  |   |||||| |     ||| |   |  |  || ||||||||||||||| || || |||||||| |||||| | ||||| || |||||||||||||| ||||||||| |||||||||| || |||||||| |||||||
ttggttattatggtattg--catttttactgt-ttgcatgctgttgtttaggtcactaatctcattcaactaatggtactgtttgggttttgctgtttaacagATGGATGCCACCACACCCAAGTACTCCAAGGCCCGTTATGATGAGATTGTGAAGGAAGTCTCTTCCTACCTGAAGAAGGTTGGATACAACCCTGACAAGA

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G153541_T06 (Zea mays), 3'ss of exon 1
-gtataatcctggtcttagt-cataaatacc--ttgctgtatgttaagattatttatttagtagctgttttctaatgatgtaagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
  | ||||     | ||| | |||   ||    |||||   ||||||| ||  |  |||  | |   |  ||  ||  | |  ||| ||   ||||     |||||||||||| ||||| || ||||| || |||||| | ||||| || |||||||||||||| ||||||||| |||||||||| || |||||||| || ||||
gttttaattagtatgttattgcatttttaatgtttgcttgctgttaaggttgctagtttcattgaactaatcgtattgtttgggttttgctgtttt-----acagATGGATGCTACTACACCCAAGTATTCAAAGGCCCGTTATGATGAGATTGTGAAGGAAGTCTCTTCCTACCTGAAGAAGGTTGGATACAACCCTGATAAGA

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: AC233866.1_FGT006 (Zea mays), 3'ss of exon 1
gtataatcctggt-cttagtcataaataccttgctgtatgttaagattatttatttagtagctgtttt-ctaatgatgtaagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
       |  ||     || |     | |   ||  | | | |   |||    ||||  | |  |  |  ||||| | |     ||     || | ||   |||||||||| || || || ||||| || |||||| | || || || ||||||||||||||||| |||||| | |||||||| || |||||||| |||||||
--gccgcctaggcgtccaggcggcggtccaacgccttgtctcacc-ttaccgctttaagaaccatgatgttaatgttattttacgttggtgttgtatttttagATGGATGCGACCACTCCCAAGTATTCCAAGGCCCGTTACGATGAGATTGTGAAGGAAGTTTCATCCTACCTCAAGAAGGTTGGATACAACCCTGACAAGA

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G001327_T03 (Zea mays), 3'ss of exon 1
----gtataatcctggtcttagtcataaataccttgctgtatgttaagattat-ttatttagtagctgttttctaatgatgtaagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
     | || |  |    | ||  |  | ||  ||  | | |   |||  |||  ||| ||    | ||      || ||  ||||  ||   || |  ||   |||||||||| || || || || ||||| |||||  | |||||||| |||||||||||||| || |||||| | ||||| || || |||||||| || ||||
tgtcctttattattccattaagctaatagta--ttattctgttccaagcatatactatctatgtaccgtg----gataatcaaagtaatggtgttctgttttttagATGGATGCAACCACTCCCAAATACTCCAAGGCACGTTATGAAGAGATTGTGAAGGAAGTCTCATCCTACCTCAAGAAAGTTGGGTACAACCCTGATAAGA

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|7924234|gb|AW830260.1|AW830260
EST:     TACTTGCCTTCACCCTTGGTGTCAAGCAAATGATCTGTTGCTGTAACAAG                         ATGGATGCCACTACCCCAAAGTACTCTAAGGGCC-GGTATGAAGAAATTGT
genomic: TACTTGCCTTCACCCTTGGTGTCAAGCAAATGATCTGTTGCTGTAACAAGgtataatcct ... ttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGG-CCAGGTATGAAGAAATTGT
EST: gi|209712611|gb|BW653744.1|BW653744
EST:     TACTTGCCTTCACCCTTGGTGTCAAGCAAATGATCTGTTGCTGTAACAAG                         ATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTG
genomic: TACTTGCCTTCACCCTTGGTGTCAAGCAAATGATCTGTTGCTGTAACAAGgtataatcct ... ttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttatttagtagctgttttctaatgatgtaagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA
                   ttctaat  putative branch site (score: 2)
                                          tttttgtt  putative PPT
                                       aaatttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatcctggtcttagtcataaataccttgctgtatgttaagattatttatttagtagctgttttctaatgatgtaagttgtgaaatttttgttgacagATGGATGCCACTACCCCAAAGTACTCTAAGGCCAGGTATGAAGAAATTGTGAAGGAAGTTTCTTCCTACTTGAAGAAGGTAGGTTACAACCCAGACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG