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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT

Basic information

species Glycine max
transcript GLYMA05G05460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 3
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaa-tagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT----
                             ||  |||    || |   || ||   ||| | || || | |  ||| | |  |||    |     || |  ||||||||||||| |||||| | |||||||| || || || ||||| |||||||| |||||||| || |||||||| ||     
-----------------------------gtatattctgctt-tctctagtatttttctactacttcccttcatcatgtaacatcc-cctgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAA

upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g45970.2 (Oryza sativa), 3'ss of exon 3
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattc-aatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
                             ||  |||    || |   || ||   ||| | || || | |  ||| | |  |||    |     || |  ||||||||||||| |||||| | |||||||| || || || ||||| |||||||| |||||||| || |||||||| || 
-----------------------------gtatattctgctt-tctctagtatttttctactacttcccttcatcatgtaacatcc-cctgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATA

upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g43470.1 (Oryza sativa), 3'ss of exon 3
gtactgatttcacaacatagtactttcctgtccatttattttataa-ataatagcattcaatagtttcatatatcctttctcattggtccactgttg--tttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
    ||| |   | | ||   |  | |||    ||||||  | |    |  |   | ||      ||| |      ||||| |    |  | | |    | |||||||||||||||||||| || ||||| || |||||||| ||||| || || || || ||||| || || ||||| |||
---gtgagtcatcca-attccatctgccttataatttatcatctgctgtcttcatactctgcttcttctttacatgtttctgaaaattttattttcaactgtcacagACCATGGCATGGATACTAGATGAATACTCAAAGTTCCATGGCCACTCCCCAGCTGTTGTCACGGGAAAGCCAATT

upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 3
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
     |    |  |||||  | ||||  |||   ||| |||| ||           |||    | |  | | || ||| |   |  |   |  ||||   |||||||||||||||||| || |||||||| || || |||||||| || || || ||||| || || |||||||| || 
-----gtaggcctaacat--tgcttt--tgttatttttttttgta--------tgctcagctatcttgtttttcatttgtaccttttatgcaattgtg--acagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATA

upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G427097_T02 (Zea mays), 3'ss of exon 3
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT-------------------------
     |    |  |||||  | ||||  |||   ||| |||| ||           |||    | |  | | || ||| |   |  |   |  ||||   |||||||||||||||||| || |||||||| || || |||||||| || || || ||||| || || |||||||| ||                          
-----gtaggcctaacat--tgcttt--tgttatttttttttgta--------tgctcagctatcttgtttttcatttgtaccttttatgcaattgtg--acagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAGTAAGTGAAAAAATGTGGCAGCAAG

upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 3'ss of exon 1
--------gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcct--ttctcattggtccactgttgtttc--acagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
         | |||| |  |  |  ||||  | |||| ||||   |    | ||||| |  |  |      |||| |  |      || |  ||     ||| | | ||   |||||| |||||||||||||| ||||| || |||||||||||||||||||||||||||||||| ||||| ||||| |||
gttttccattcctgaatctaatatgtagtg-tgtcctttccaggaa---aaaaaatattgactctttgacctttctttaacttgaattttactttccttactctcgatttggacagACGATGGCATGGATTCTGGATGAATACTCAAAGTTTCATGGGCATTCACCTGCAGTTGTTACAGGAAAGCCAATT

upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
||  |  ||||||    |  |  | |    |  |||| |  | |   |  |    ||  | ||||  || | |  ||| |            |||  ||||||||||||||| |||||||| |||||||| || |||||||||||| | || || ||||| || || || |||||  ||
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttg----------gtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT

upper sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
                    |  |||| | | | ||| || | |   |  |    |||  |  || || |  |   || |||||  |    ||||  ||||||||||||||| |||||||| |||||||| || |||||||||||| | || || ||||| || || || |||||  ||
------------------gtttttttctttttcttttgttctttctttctt----ttctttttttgcaaagttggattttcatt--ttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT

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|9820671|gb|BE556181.1|BE556181
EST:     GGCATTCAAAAGGATGTTCCCTGCCCCTGATATGGGGAACTAATGCTCAG                         ACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTTCCCC
genomic: GGCATTCAGAGGGATGTTCC-TGCCCCTGATATGGG-AACTAATGCTCAGgtactgattt ... tgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATT-CACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
                                            ttgtttc  CT-rich tract
         aatagtttcatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG