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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggaatgccttgctattcctatgagtatcttttataccatgtttatcctgttttgagctaacttattacattgttctttttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCCGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCAA

Basic information

species Glycine max
transcript GLYMA13G17790.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 4
gttggaatgccttgctattcctatgagt-atcttttataccatgtttatcctgtt-ttga--gctaacttattacattgttctttttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCCGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCAA
||||  ||  |||    | | |||   | || |  || |  || |  | | ||||  |||  || | ||| || || || | |  |     |||||| |||| |||||||| ||||| || || |||||||| ||||| ||||||||||||||||| |||||  |  |||| ||||| | ||||||||| || |
gttg--atttcttaacttacatattcttcatatgatagaatatatggagcatgttactgatagcaatcttgtt-caatgctgtact----gcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCAATTGCCATTGGATTTGATGATTTCATTGCTGATGCTCTCAGAGGAACTGGGTACTATCAGAAGGCCA

upper sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G082924_T01 (Zea mays), 3'ss of exon 4
gttggaatgccttgctattcctatgagt--atcttttatac-catgtttatcctgttttgagctaacttattacattgttctttttctaa--cagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCCGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCAA
|||   ||   || || ||   ||      | |   ||||  ||    ||  |  |  || | |  || |      |     |  |  ||  |||||| |||||||||| || ||||| ||||| || || || ||||||||||| || |||||||| |||||  || |||| ||||| ||||| ||||| || |
gttc--ataatttactgttttgattgcctaaacagatataggcacagctagacattactgcgttgtctaacattcctacatgtcctgcaatgcagAGGCTGGTTTATGGGGCCAAGGCGGAGGCTGCCATCGCCATTGGGTTTGACGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA

upper sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
-------gttggaatgccttgctattcctatgagtatcttttataccatgtttatcctgttttgagctaacttattacattgttctttttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCCGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCAA
       || | ||    |  ||| ||  |     ||||||   | ||| || ||    | |     | | |  | |  |   |  || |  |||||||||||||||||||||| || ||||| ||||| || || || ||||||||||| ||||| || ||||| ||| |||| || ||  | || |||||| | |
gtaagatgtcgaaacaagt--ctactcacaaacccatctttctaatcat-ttcatt---tatcacaatgagtactcatgtctctacttgta-aacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA

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|298174641|gb|HO014672.1|HO014672
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttggaatgc ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|37994915|gb|CF806504.1|CF806504
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttggaatgc ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccatgtttatcctgttttgagctaacttattacattgttctttttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCCGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCAA
                      agctaac  putative branch site (score: 2)
                                   cattgttctttttct  putative PPT
                         taacttattacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggaatgccttgctattcctatgagtatcttttataccatgtttatcctgttttgagctaacttattacattgttctttttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCCGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA