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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

Basic information

species Glycine max
transcript GLYMA13G42800.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
ctttatgtctaca-tgattttgtg-cac-attttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| | ||  | |  |||   | |   || |  |  || |  || |  |    | ||    |   | | |||    ||| | | || ||| |  |  |  |||| || || || || | ||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||
ctgtgtgagttctctgaacctataatactacctgcttctgtatattttcaaatcatgagcatgaagctaatacc-atgttctcatattgtt--ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttc--cagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
   | ||   |  || || |  |  |||||   ||     |    |    ||     |  |    |       || ||    || |  |  | | |||  ||| ||||| || |||||||||||||| |||||| |||| ||||||||||||||  ||||||||||||| ||||||||||| ||| ||||||| || ||| ||
---tttgctgatgtgcatctcatatacattcgattagatgtaatgtaccctttcgagttttatgtagtgacatattgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
-------ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
       |  | | ||||| || || ||    | | |||||   | || | ||    || |  | | ||  |  |||||  |     | | || |   ||  |  ||| |||||||| || | ||||||||| ||||||||||| |||||||| |||||  |||| || |  || || || || ||||||||||| || |||||| ||
ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaat----ttgtgaacattgtgctgatttgctt----ctctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
-------ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
        || ||||   |    |||| |    || || | |||   | | ||| |||||   || || | | |     |||   | |  ||| |  |   |  ||||||||| ||||| ||||||||||| ||||||||||||||||| ||||||||  | |||||||||||||| || ||||| ||||||||||| || ||||||
tgaatgagttaatgtg-gctgagttttttttggatcttatattttgctgcctgggtttattacta-tggtgatacc---atgtcctcactttgtt--ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
ctttatgtctacatgattttgtgcacatttttttt---ttaatttcatggttttatagatactgatcaaatttggatg-gtgttatgttgctcatatcttc-cagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
   ||||| | | ||||||    | ||| | || |   |||| |  |   |   ||   |    ||    |    ||   | |  |||  |   ||| | | ||| ||||| || || || |||||||| |||||| |||| ||||||||||||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
---tatgt-tgc-tgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
------ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttat-agatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
       |||    ||     || ||      ||  |    ||  ||  || ||  |||  | || ||||  |  ||        || |  |  | || ||  | || ||||| || || || |||||||| |||||| |||| |||||||| |||||  ||||||| |||||||||||||| |||||| ||||||| |||||| ||
ttgctgatttgcacctcttatatcttaaatgtatgctgccattttttgtattgtcctattgggtagtgatatatattat------ttgtaatctttatttcaac-agTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
-ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcat-atcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
    |||  || || | |   |    ||  |  || || | |       ||| | |  | ||     ||    ||  | || | ||  |  | |     ||| ||||| || || ||||||||||| |||||||| ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| ||
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatat--tcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctc----atatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
     | |   | |  |           ||  |  | |||||||    ||       | || |    |     ||||  |   | | ||    |  | || ||| || || ||||| || || || || |||||||||||| ||||||| |||||  ||||||||||||| || ||||| |||||||||||||| |||||  ||
----ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
-----ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
      ||  | || | | | |     ||   || ||   |  | ||  ||  ||| || |||| || ||   |    ||  | ||   |  || |||  |   ||||| |||||||| || || || || |||||| ||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| 
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttt---tctcttataatt---agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG

upper sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
-----ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
       |  | |  | |  ||  |      |  || ||| |  | || |  ||   ||     |  | |||||| | || |    |||| |||      ||||| ||||| ||||| || |||||||| ||||||||||||||||| ||||||||| ||||||||||||| ||||| || |||||||||||||| |||||||||
gaaagactattatggaaacaatgctaatggtaacttgtttatt-tctcttatttgggtacgatttagtgaaattttgctgat----tgtttctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

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|207847156|gb|GD820803.1|GD820803
EST:     GCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAA
genomic: GCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|208327646|gb|GE119368.1|GE119368
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|7686354|gb|AW757002.1|AW757002
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|207758381|gb|GD727307.1|GD727307
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|208191779|gb|GD994625.1|GD994625
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|19936402|gb|BQ080848.1|BQ080848
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|207770869|gb|GD743421.1|GD743421
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|207752398|gb|GD725819.1|GD725819
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|207701978|gb|GD683852.1|GD683852
EST:     GCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAA
genomic: GCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
EST: gi|21887329|gb|BQ740542.1|BQ740542
EST:     GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG                         CGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA
genomic: GTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
           tactgat  putative branch site (score: 2)
                                             tatcttcc  putative PPT
                atcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

- - - - -tacatga
- - - - - - - - - - -tgcacat
- - - - - - - - - - - - - - - - - - - - ttcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct