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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT

Basic information

species Glycine max
transcript GLYMA07G00420.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 5
--------------aactttttga-ttcattaattttcatgtttatgttatttggagccttgcctaaccattat--tatatatgaa---tattatcatggaacacttgtcttctt-----------cacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
              ||     ||| ||| |  ||| |  ||      ||||| |    |   |  ||| ||  |  || ||||| |   | || |||  | |  |||   |  ||            ||||||||||||| ||||| ||||| |||||||||||||| |||   |||||||||||| ||||||| ||||||| |||||||||||| ||||| || ||||| 
gtaaactgagcaaaaataccctgagttcttctattatagtgaaagcattattggcttgcaatctgaactatagttctacatatgcactctgttgtcagtgtaggcttaattgtttggttaacatattacagGGAACATGCACCATCCATTATTTTCATGGATGAAATAGACTCCATTGGATCTGCTAGGATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTCCAGCGA

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 5
--aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
  ||    ||  |   || |     |  |||           | |  |   || |  | ||| |      |  || |  |       |    |  |   |||||||||||| ||||| ||||| || |||||||||||||||  ||| ||||||||| | ||||| ||||||| |||||||||||||||||| || ||||||
acaaggccttagtgagttgaagcataactttgcacatgcacaatctgttattatctttcattgtgggcttagtttgttttatctggttcacttatt--gcagGGAACATGCGCCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGATAGTGAAGTGCAGCGT

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
----------aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
                ||||  ||| | ||| ||| || || || | |      | || |   |||| |    |  |  | |||||  ||  ||||| |        |||||||||||| ||||| ||||| || |||||||||||||||  ||| ||||||||| | ||||| ||||||| |||||||||||| ||||| || ||||||
attagttgtttgtgagttgaagcataattttgcatattcatattctgtta---ttagctttttcattgtgggcttagtttgttatcg-ggttcacttatt------gcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
-----aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
      |       || ||  | |  |||| || ||  |  |   |        |  |   ||   ||  |   || || |   |    ||| |  | |||  ||||| ||||| |||||||| ||||||||||||||||| || ||||| || |||||||| ||||||||||| ||||| || ||||| |||||||| ||  | 
gtaatgagcaaagtatacaccattaatcatcttcattgtgctgaaaaatacttattccagctagcttacctttctagtacctctgg---cttatggttttc--agGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 5
---aactttttgattcat-taattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
   |       |  |||| |||    ||  ||     ||  ||      | | |    | || | | |       ||  | |  | |  || | |  ||  |||||| ||||| |||||||| ||||||||||||||||| || |||||||| |||||||| ||||||||||||||||| || ||||| |||||||| || || 
cacagtgccaagtctcatgtaaggagcaaattacaaataggtgagatgattcgttgaaaatactctttccag---ttggcttacaccggtt-tatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATTGGGTCTGCTCGTATGGAATCTGGAAGTGGAAATGGTGACAGTGAGGTGCAACGG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
aactttttgattcattaattttcatgtttatgttatttggagccttgcctaacc-attattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
           |||| ||   | |     | |  |     |   |||| |      ||  | | | |  | | | |  |     |  | ||||  | ||||||| ||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||| || ||||| 
-gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------------------------------------aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgt--cttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
                                                                                                    || | |||      | |  |||  |   |  ||||||        |    || |    || ||| |     ||||  |        ||   |||  | ||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||| ||| || ||||||||||| || ||||| 
gtttgtttaatatctttagtggaaaccatgacttgtgatacacctagaggatttatttttcactcataagataatattttatatgttacctctcctgggtaattgtttag--agtcacatttttttcctgggttattgaattttgttttaaatctcccttttatcttgtccttatggtctcttctctgctgctttattacagGGAGCATGCTCCATCAATCATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGAATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGA

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 5
------aactttttgattcattaattttcatgtttatgt-tatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
         |||||||||    |          || | | ||  ||||  |||  |    ||  |   |||| || | ||| || |  |   |||| |  ||   ||||||||||| |||||||| |||||||||||||||||||| ||||||||||| |||||  |||| ||||| | |||||| || |||||||| || ||||| 
taagatgtgtttttgatt-gccatcaacggaacttgtctctacctggaaactt--catgtcaagaacgtataaga-tgttaacaagttatttttgtatggtt---agGGAACATGCACCATCAATCATCTTCATGGATGAAATTGATAGTATTGGATCAGCTCGTGTGGAGTCTGGGAATGGCAATGGAGATAGTGAAGTTCAGCGG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 4
aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacact-tgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
                                         |  | |      |  |||| |||   | |||  | | |     || ||| |||||   || || ||||||||||| |||||||| ||||| || |||||||| ||||| ||  | || ||||| ||||| | ||||||||| || ||||| || ||| | 
-----------------------------------------gtatcgtaatgtccatattctatcctagtatagttacgtttttctgtgttttctt---agAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28638 (Selaginella moellendorffii), 3'ss of exon 5
aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacact-tgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
                                         |  | |    | |  |||| |||   | |||  | | |     || ||| |||||   || || ||||||||||| |||||||| ||||| || |||||||| ||||| ||  | || ||||| ||||| | ||||||||| || ||||| || ||| | 
-----------------------------------------gtatcgtaatatccatattctatcctagtatagttacgtttttctgtgttttctt---agAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA

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|37995024|gb|CF806613.1|CF806613
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|192332825|gb|FK026826.1|FK026826
EST:     TTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|254318622|gb|GR832790.1|GR832790
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|15589715|gb|BI674331.1|BI674331
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|16284294|gb|BI946006.1|BI946006
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|16277739|gb|BI942538.1|BI942538
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|209727795|gb|BW658719.1|BW658719
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAAC-TTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|18039807|gb|BM308101.1|BM308101
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATG
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATG
EST: gi|16281818|gb|BI944685.1|BI944685
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
EST: gi|208125966|gb|GD925994.1|GD925994
EST:     TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAG                         GGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctc ... ttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
 gcctaac  putative branch site (score: 2)
                                     cacttgtcttcttc  putative PPT
     aaccattattatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttgt