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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA

Basic information

species Glycine max
transcript GLYMA18G02210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
| ||| | | | | ||||| | ||| || | | | || | ||| | || || |||| ||||| |||| ||||| || ||||| ||| ||||||| ||||| ||||| || ||||||||||||||||||||||| ||| ||||||||||||| ||||||| ||| ||||||
-----------------------------------------atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatggttatgaaaaaaatt------cagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA

upper sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 3
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctg---ttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
|| || ||| || | | | || | | || || || | || | | ||| | || | || | || | |||| || || ||||||| ||||| || || ||||| ||||||| |||||||||||| || |||||| ||||||| |||| | |||||||| ||||||
-------------------------------------------------atgtcaatttga-gatacaaacataccagaattgatgaatcgtaatactttgagacaggcagacactgatgatgataattaatttgattcggtttttgaagGTAAACCCAAACGACATCGTGTTCGGTGGGTGGGACATCAGCAGCATGAACCTGGCCGACGCCATGACCAGGGCTCGGGTGCTGGACATCGACCTGCAGA

upper sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 3
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggag-tgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
||| || || | || | | | | | || | || || || | ||||| | || || | | || | | || ||| ||||| || || |||||| |||||||||| || ||||| ||||||| |||||||||||| ||||||||| ||||||| |||||| | ||||| || ||||||
------------------------------------------tgggcagtactgacagacggtggtgctaactggttgtaaatcctcaaacttttgaggtcttgttttcatgaccaagtt---gaact---attgaactggttttcagGTGAACCCAGACGACCTTGTGTTTGGAGGCTGGGACATCAGCAGCATGAACCTGGCAGATGCCATGACCAGGGCCAAGGTGCTGGACATTGACCTGCAGA

upper sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 3
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
| | ||| |||| || | ||| | | | | | | |||| | | | ||| || | | || ||| ||||| || || |||||||||||||| || || ||||| || ||||||||||||||||| || ||||| ||||||| |||||| | || || || ||||||
----------------------------------------------acactcgtgcagtattgacgatggtgctaactggttgcagattcgcag-actcggtgtttgttatcttcttttcatgaccaagtgttgaactggttttcagGTGAACCCAGACGACATTGTGTTCGGAGGCTGGGACATTAGCAACATGAACCTGGCCGACTCCATGACCAGGGCCAAGGTGCTGGATATTGACCTGCAGA

upper sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 3
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
| ||||| | | | |||||| | || ||| || | | || || | | ||| || | ||| | ||| | ||||| || || || |||||||| |||||||||||||| ||||| ||||||||||||| ||||| ||||||||||| ||||| | ||||| ||| ||||||
----------------------------------------gtaagttagtaactcaatt--tcattgaaaatatttgcatgtgtggaaa-gcattatttgatttatttatagtatga--tataattt----atattataatgatcagGTGAACCCAGATGACATTGTTTTTGGGGGATGGGACATCAGTGACATGAACCTGGCAGATGCAATGGCCAGGGCTAAGGTCCTGGACATTGATCTGCAGA

upper sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 3
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
||| | | || | || ||| || ||| | | ||| ||| ||||| ||||| ||||| |||| |||||||||||||||||| |||||||||||| || |||||||||| | || || || || ||||| || | ||||
-----------------------------------------------------------------------------------gtaactaacaacaatcaaaga---tggttcttgagttttggtttct---tgtatcacttg-cagGTGAATCCCGACGATGTTGTTCTTGGGGGATGGGATATCAACAACATGAACCTCGCAGATGCCATGGAGCGAGCGAAAGTTTTGGACATGGACCTCCAGA

upper sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ27629 (Selaginella moellendorffii), 3'ss of exon 3
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
||| | | || | || ||| || ||| | | ||| ||| ||||| ||||||||||| |||| |||||||||||||||||| |||||||||||| || |||||||||| | || || || || ||||| || | ||||
-----------------------------------------------------------------------------------gtaactaacaacaatcaaaga---tggttcttgagttttggtttct---tgtatcacttg-cagGTGAATCCTGACGATGTTGTTCTTGGGGGATGGGATATCAACAACATGAACCTCGCAGATGCCATGGAGCGAGCGAAAGTTTTGGACATGGACCTCCAGA

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|4296509|gb|AI442485.1|AI442485
EST:     CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATG                         GTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC
genomic: CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATGgtatcattac ... ctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC
EST: gi|9986214|gb|BE660322.1|BE660322
EST:     CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATG                         GTTAATCCTGACGACATTGTGTTTGGGGGATGGGA
genomic: CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATGgtatcattac ... ctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGA
EST: gi|27427007|gb|CA938527.1|CA938527
EST:     CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATG                         GTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC
genomic: CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATGgtatcattac ... ctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC
EST: gi|6667615|gb|AW279066.1|AW279066
EST:     CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATG                         GTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC
genomic: CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATGgtatcattac ... ctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC
EST: gi|120530142|gb|EH258276.1|EH258276
EST:     CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATG                         GTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC
genomic: CCTTCCAGGGAGAGGAAATCTATGCCCCATTCAAGAGTCTGCTTCCAATGgtatcattac ... ctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA
              ttgtaac  putative branch site (score: 2)
 ttgaaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG