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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

Basic information

species Glycine max
transcript GLYMA14G02530.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
------gtatgttttcta-attactgaagtatagacta--gctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG
           | || |  | | ||||||  |  ||||  ||| |||  | |   |   |||| |  ||   ||  ||    |  |  ||| ||||||||||||  ||||| ||| | || || ||||||||||| ||||||||||||||||| || ||||||||||| ||| | || |||||  | |||||||
gtactgaccaatcttgtgtactgctgaagc-tgaactattgcttggtaattttactaatatattca-atgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG

upper sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG
   | ||| | | |  || | |  | |   ||||       |    ||| || |         ||  ||||  |     || ||||||||||||  |||||| ||| | ||||| ||||||||||| ||||||||||||||||| || ||||||||||| ||  |||| |||||  | |||||||
--gtatttgccagt--cttaggcgttgcaaagcttttgcaccatacttttatgtggctg---gctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG

upper sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 10
gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG
  | | |   || |  || | || | |   ||||       |     || ||||        | ||||  |  | |   ||| |||||||||||  |||||| ||| | ||||| ||||| ||||| ||||||||||| ||||| || ||||||||||| ||  ||||  ||||  | |||    
tcaaggtacttagt--cttatgtgttgcaaagcttttgaaccatacatttatatggctggctaattttatttattt---tgTCAGGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCT----

upper sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 10
gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG
    ||  |     |  ||   |  | |     ||     |   |||   ||||        | ||||  |  | |   ||| |||||||||||  |||||| ||| | ||||| ||||| ||||| ||||||||||| ||||| || ||||||||||| ||  ||||  ||||  | |||||||
----gtacttagtcttatgtgttgcaaagcttttgaaccatacattt---atatggctggctaattttatttattt---tgtcagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTG

upper sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 7
--gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcc----tcatacactttttatggtc-tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG
   ||   || || |||  |  |   ||      |   |       |   ||||| |     | |||| || ||  | ||  ||  | | ||||||||||||  || || || ||||| ||  |||| |||||||| ||||| || |||||||| ||||||||||| ||| | |||||||| || |||||||
gtatacacttacttatttttcgatattaataatacaatgccagagttaaatgatagcaaaaataataccctattcttcgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG

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|58018648|gb|CX705390.1|CX705390
EST:     TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA                         GCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
genomic: TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAAgtatgttttc ... tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
EST: gi|23732448|gb|BU764383.1|BU764383
EST:     TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA                         GCTGCTGNTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
genomic: TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAAgtatgttttc ... tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
EST: gi|15589596|gb|BI674212.1|BI674212
EST:     TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAT                         TCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
genomic: TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAAgtatgttttc ... tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
EST: gi|17518632|gb|BM187674.1|BM187674
EST:     TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA                         GCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
genomic: TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAAgtatgttttc ... tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
EST: gi|7588263|gb|AW704062.1|AW704062
EST:     TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA                         GCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
genomic: TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAAgtatgttttc ... tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGAT
EST: gi|193696238|gb|FK639260.1|FK639260
EST:     TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA                         GCTGCTGTTAATGCACTCCAACNTCAGCCGATTGTCAATG
genomic: TTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAAgtatgttttc ... tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG
               ttttgat  putative branch site (score: 4)
                                           tctccat  putative PPT
              tttttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT