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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctccacgagcaagtgatggaatgctgcacgctgttaaagcctaatggtccatttcacacagagagattggatctatatacatttt...

Basic information

species Glycine max
transcript GLYMA07G09180.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G09180.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g14010.1 (Oryza sativa), 5'ss of exon 5
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctccacgagcaagtgatggaatgc-tgcacgctgttaaagcctaatggtccatttcacacagagagattggatctatatacatttt
|||||||| || |||||  ||  |||  | ||||| |||||||||||||| | |||||||||||||||    | ||||   |||       |       |  ||| ||   || ||    |  ||||        | | | | |    ||     ||| |  ||   
ACTGACACAGCGTCTGTACTGCAAGAGACCATTGGCTATATCAGATTCCTCCTGAGTCAAATTGAGgtccaatctctctctctcactttctatagctctgtctgcgtgtgtgc-gtgtgtgtttaatttagagggtgaaaaaaaatacttcccgttatttttatcaa

upper sequence: GLYMA07G09180.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G105494_T02 (Zea mays), 5'ss of exon 5
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctc-cacgagcaagtgatggaatgctgcacgctgttaaagcctaatggtcca-tttcacacagagagattggatctatatacatttt
|||||||| || |||||  |  | ||||| |||||||| ||||||||||| || ||||||||||||||   | |  ||   ||| ||| | |      |      |    || ||   | ||||   |  |     ||| || |    |  | |     || |||   
ACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAGgtccagctcttctctctcacaccatctttctctctctctccatgcg-tgcccatgcctgcagccctggcctcaaactgtagcacagtacaaggat-cataga

upper sequence: GLYMA07G09180.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G072238_T03 (Zea mays), 5'ss of exon 5
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctccacga----gcaagtgatggaatgctgcacgctgtta---aagcctaatggtccatttcacacagagagattggatctatatacatttt
||||||||||| |||||  ||  |||  | |||||||||||||||||||| | | |||||||||||||   || ||||   |||   |        |   ||   | || | | |   | |   ||   ||||     || |  | |||    |  ||    | |  |     
ACTGACACGGCGTCTGTGCTGCAAGAGACCATTGGGTATATCAGATTCCTCCTGGGTCAAATTGAGgtccagtctctctctctctctgtctgtctgaaccatcagaagcagtatgggttcacataaaattaataaataatgtggc-cagccccaccggccaca-acgc-----

upper sequence: GLYMA07G09180.3 (Glycine max), 5'ss of exon 4
lower sequence: AT2G20100.1 (Arabidopsis thaliana), 5'ss of exon 5
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcct--ccacga-gcaagtgatggaatgctgcacgctgttaaagcctaatggtccatttcacacagagagattggatctatatacatttt
|||||||| |||||||||||||  || |||||||| || || |||||||| || ||||||||||||||||  | |||  |||   | || | ||   | ||   ||      |      ||    || | |    || | ||||   | |    |   |||  ||||| 
ACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAGgtgacttgtcttttccaaactaccatgcttcttatttcatttatttcaagacaaatatttatttgaatcttcctcacaactaca--acacaaataatcattt-

upper sequence: GLYMA07G09180.3 (Glycine max), 5'ss of exon 4
lower sequence: AT4G29100.1 (Arabidopsis thaliana), 5'ss of exon 5
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctccacgagcaagtgatggaatgctgcacgctgt---taaagcctaa---tggtccatttcacacagagagattggatctatatacatttt
|||||||| ||||||||| |||  ||||||||||| || || |||||||||||||||||||||||||||    |  || |   | |    ||| |  |   || | | |   |     ||| || ||    |  ||| |||  || | | | |  | |   | | |      
ACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcgtcttttccaaactccaaatattctcattcagtaaaataaaaataatgcttatgattactccgtttaccaaaaaaaaaaagaagaaaaaaa------

upper sequence: GLYMA07G09180.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 5'ss of exon 5
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctcc----------acgagcaa--gtgatggaatgctgcacgctgttaaagcctaatggtccattt-cacacagagagattggatctatatacatttt---------------------
|||||||| || ||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||| | | |||          || | |||   |||   | |  ||   |           ||| | | ||||| ||   |  ||  ||  |  ||||| |  ||                      
ACTGACACAGCTTCTGTCTTGTTAGAAGCTATTGGTTATATCAGATTCCTCCAGAGTCAAATTGAGgtgatgtttcttcccttccttttatttttacaaacaaccatgaactagtagtgacgggcacaggtttttaaagcttcattttcagttattgaagttctaaatatattcccttctcttatccccctaaaatgcag

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|120493651|gb|EH221818.1|EH221818
EST:     TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
EST: gi|19348059|gb|BM892591.1|BM892591
EST:     TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
EST: gi|192312979|gb|FK004625.1|FK004625
EST:     TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
EST: gi|208239088|gb|GE037166.1|GE037166
EST:     TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
EST: gi|23053843|gb|BU577597.1|BU577597
EST:     TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
EST: gi|192312980|gb|FK004626.1|FK004626
EST:     TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
EST: gi|21677113|gb|BQ629464.1|BQ629464
EST:     TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
EST: gi|19348345|gb|BM892877.1|BM892877
EST:     TCTTGTTAGAAGCTACTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG                         GCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA
genomic: TCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttc ... ttggatgcagGCTCTTAGCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctccacgagcaagtgatggaatgctgcacgctgttaaagcctaatggtccatttcacacagagagattggatctatatacatttt

- - - - - - - - - - -  AGAAGC