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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaattctcattgaatgactagttttatctcattgataactagagaaggaatatttttgttttagcatttgattttttttttcctgttggttttcctagGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCAACATTGCAATGCCTCCATTCTGTGCCTGAGTTAAAGTCAGCTTTGACTA

Basic information

species Glycine max
transcript GLYMA07G01480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 4
attaattctcattgaatgactagttttatctcattgataactagagaaggaatatttttgttttagcatttgattttttt-------tttcctgttggttttcctagGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCAACATTGCAATGCCTCCATTCTGTGCCTGAGTTAAAGTCAGCTTTGACTA
   || |  | |   |   ||| || ||| |     ||||  |     |   |||||| || ||   | |   |  |          ||||   ||||  || | |||| || | |||||||||||  |||||||| || |||||||| |||||||| || ||||| ||||| |||||||| || ||| | |||||||||||    |
---aaattgcttaagagcgcta-ttatatttggc--ataagcatgttggtcttattttggtgttcttaatctgtgctgcaagtgagatttctctttggaatttc-agGGACACAGTGCTGGTCTTTATAACTTGGGGAATACATGTTACATGAATTCCACTTTGCAGTGCCTGCATTCTGTTCCAGAGCTGAAGTCAGCTTTATTGA

upper sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017086_T01 (Zea mays), 3'ss of exon 4
attaattctcattgaatgactagttttatctcattgataactagagaaggaatatttttg-ttttagcatttgattttttttttcctgttggttttccta-------gGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCAACATTGCAATGCCTCCATTCTGTGCCTGAGTTAAAGTCAGCTTTGACTA
       ||  | |  |   |  |   || ||| ||||             ||  ||||| |  ||| ||||    | |||  |    |  ||| |||||       ||| || | |||||||||||  ||| | || || ||||| ||||||||||| ||||||||||| || |||||||| || ||| | ||||||||  ||   |
-------cttgtcgtttctatgatca-atatcaatgatgttacctttttttatccttttggtgctagtatttatcatctttactgaaatgagttgtcctaatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA
















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|193699037|gb|FK641256.1|FK641256
EST:     GAACTGTTTTTGTTGAAGATCTTCCTGAAGAAGAACAAGTAGTTGCTGTT                         GGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCA
genomic: GAACTGTTTTTGTTGAAGATCTTCCTGAAGAAGAACAAGTAGTTGCTGTTgtaagtttca ... gttttcctagGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCA
EST: gi|18040402|gb|BM308696.1|BM308696
EST:     GAACTGTTTTTGTTGAAGATCTTCCTGAAGAAGAACAAGTAGTTGCTGTT                         GGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCA
genomic: GAACTGTTTTTGTTGAAGATCTTCCTGAAGAAGAACAAGTAGTTGCTGTTgtaagtttca ... gttttcctagGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCA
EST: gi|298175291|gb|HO018172.1|HO018172
EST:     GAACTGTTTTTGTTGAAGATCTTCCTGAAGAAGAACAAGTAGTTGCTGTT                         GGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCA
genomic: GAACTGTTTTTGTTGAAGATCTTCCTGAAGAAGAACAAGTAGTTGCTGTTgtaagtttca ... gttttcctagGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaggaatatttttgttttagcatttgattttttttttcctgttggttttcctagGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCAACATTGCAATGCCTCCATTCTGTGCCTGAGTTAAAGTCAGCTTTGACTA
                      atttgat  putative branch site (score: 5)
                            ttttttttttcctgtt  CT-rich tract
     aatatttttgttttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaattctcattgaatgactagttttatctcattgataactagagaaggaatatttttgttttagcatttgattttttttttcctgttggttttcctagGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCAACATTGCAATGCCTCCATTCTGTGCCTGAGTTAAAGTCAGCTTTGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - tgaatga