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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG

Basic information

species Glycine max
transcript GLYMA08G13680.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 3
gtgagaaaattcaagcatccttgttttttgagttattgt-ctaatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
|| ||  |||| |        ||||  | || ||    | ||  |||||  ||    |      |||    |    | ||| | ||  |  |    |||  |||  | ||||| |  ||||| ||||| |||||||||||||||||||||||||| || ||||||   || |     |||||| | ||  |
gtcagccaattta-------ctgttcctcgacttgccattctgttgttgccgtgcactggatggtaaaactaacactatttatcttacgcctt--tcagAATGAGACTCAGGACTTCCTTTTCATTGCGACTGAAAGATACAAATTCTGTGTTCTGCAGTGGGATGGAGAAAAATCGGAGCTTCTCACTAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g51480.2 (Oryza sativa), 3'ss of exon 3
gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
                                                               |||    |    | ||| | ||  |  |    |||  |||  | ||||| |  ||||| ||||| |||||||||||||||||||||||||| || ||||||   || |     |||||| | ||  |
--------------------------------------------------------------gtaaaactaacactatttatcttacgcctt--tcagaatgagactcaggacttccttttcattgcgactgaaagatacaaattctgtgttctgcagTGGGATGGAGAAAAATCGGAGCTTCTCACTAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 3
gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
|| ||  |||| ||   || |   |    ||    || | |  | ||||    | || ||  ||||    ||||||| | ||| ||  ||     |||  |||  | ||||| | |||||| ||||| || || || ||||||||||||||||| ||||||||| | || |     |||||  | ||  |
gtaagctaatttaaagttcatccatccgagatactttatttgtttttgtgaagtattttt--ataaatggattttttctgtttgtttcttatcctcagAATGAGACTCAGGACTTTCTTTTCATTGCTACGGAGAGGTACAAATTCTGTGTTCTGCAATGGGATGCAGAAAAGTCAGAGCTAATCACCAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttt-tttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
             || ||  || | || |    || | |    |||   || |  | | |   |||     ||  ||  |     ||  | |    ||||||||||| || || | | | ||| |||||||||||||||| |||||||||||||||||||||||||  ||| |   ||||||| ||||| |
----------gtgagtatagttttcttattgaatacttttctctgtctgaggtaatacgtaagtaacaatgttaattgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagaaaattcaagcatccttgt-tttttgagttattgtct-aatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
  | ||  ||  |    |  |||| || ||  || || |||| |||  || ||||      |  ||| | |  |      | |||| |          |||| |||||||| || | | | || ||||||||||| |||||||||||||||||||||||||||||| | ||| |   ||||||| ||||| |
--gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatg-agttaaaatgttgatagtattgtccaccgtcttttgt----------agGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 3
gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaattttttttt--ttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
|| || |   ||  |   | |   |       ||| |   ||   || || |  |   ||  ||  |   | | ||  ||  | |||||| ||| | ||||| ||||| || |||| ||| || || ||||||||||||||||| || |||||||||||||||||| | |||| |  |||| || ||||| |
gtaagtatcatcttgtgacat--atagaaagcttacttagtagcattataatcatgctttttatgctaatactattgcttgctgttttggattctaacagGGCGAAGCACAAGATTTTCTATTCATCGCAACTGAAAGATACAAGTTTTGTGTTCTTCAATGGGATGCAGAGAATTCTGAGGTTATTACAAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 3
-----gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
      | |    | |    || | | |   |  | | ||   | | |  || ||     |  |  |  || | ||  ||| || || |    ||   || |||||||  | || ||    || |||||  |    |||||||| ||||| |||||||||||||||||| | || || ||    | | |||||||
ggttccttatcgtacttgt-caacatggaactcagcgctagcatatgaacttataaaaaata-tgacgcaacgaaaactttattgttgtgcttttcttac-agGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG

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|209714348|gb|BW665598.1|BW665598
EST:     ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCAT                         GGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
genomic: ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCATgtgagaaaat ... tttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
EST: gi|213615293|gb|DB963487.1|DB963487
EST:     ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCAT                         GGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
genomic: ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCATgtgagaaaat ... tttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
EST: gi|213589389|gb|DB961722.1|DB961722
EST:     ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCAT                         GGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
genomic: ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCATgtgagaaaat ... tttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
EST: gi|213590572|gb|DB968122.1|DB968122
EST:     ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCAT                         GGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
genomic: ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCATgtgagaaaat ... tttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
EST: gi|209717579|gb|BW679686.1|BW679686
EST:     ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCAT                         GGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
genomic: ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCATgtgagaaaat ... tttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT
EST: gi|209723170|gb|BW675116.1|BW675116
EST:     ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCAT                         GGTGAAGCGCAGGATTATCTTTTTATTGCAACTGANAGATACAAATTCTGT
genomic: ATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGCCCTCATgtgagaaaat ... tttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG
                            tttttttttttttttg  CT-rich tract
     tagttttttcttccat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT