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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttgttgtttttttcccctccttctgagtaactactaatttctcttctttgtttgatatatttaaccattgattatatcttttttcctccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGAC

Basic information

species Glycine max
transcript GLYMA04G39490.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 5
tttgttgttgtttttttcccctccttctgagtaactactaatttctcttctttgtttgatatatttaaccattgattatatcttttttcctccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGAC
| ||  |||  |   |   |  ||   ||  |   |  |   ||   | |||  | |   |   | |||  |    |     | | ||  | |||| |||| ||| || |  ||||||||  | |||||||||| ||| || || |||||| ||||||||||||| || |||||||| || |||   || |||||||| |
tatgcagttcctgcctgtacaaccacatgcatccatgattgatttaatacttaatctttcactctaaactctgaggtgaccatctattgttgcattgcagACAGACAAAGGTGATGAAGAATTGTGTAGTGTTTATGTGCCAACCAATCATTTATATATTGGTGACATCTTTTTGGTAAACTCCGCCGAAATTATAAGGC

upper sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 5
tttgttgttgtttttttcccctccttctgagtaactactaatttctcttctttgtttgatatatttaaccatt--gattatatcttttt-tcctccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGAC
    |||   |   | |          |  ||   || |  | |     ||   ||||| | |||  |   ||  | || |   | ||  |  |  |    ||||||| || ||||| |||||| | || |||||||||||||| || || |||||||| ||||||||||||||| | || || ||||| || || || ||||
---attggattacatatattacagcgttatgtttttaatgttgttgaggctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC
















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|254330499|gb|GR841764.1|GR841764
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|254349027|gb|GR860299.1|GR860299
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|9564106|gb|BE473615.1|BE473615
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTTGTTTT-GTCCCTACGAATCA
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGT-GTTTTTGTCCCTACGAATCA
EST: gi|151407101|gb|EV276916.1|EV276916
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|151397141|gb|EV267014.1|EV267014
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|151405159|gb|EV274973.1|EV274973
EST:     GTGTTGGTGAATATGCACTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|254330500|gb|GR841765.1|GR841765
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|31466200|gb|CD408228.1|CD408228
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|31459279|gb|CD401307.1|CD401307
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
EST: gi|31561519|gb|CD487357.1|CD487357
EST:     GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG                         AAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT
genomic: GTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAGgtactgtgta ... tccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctttgtttgatatatttaaccattgattatatcttttttcctccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGAC
                              ttatatcttttttcct  CT-rich tract
         tttgatatatttaacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttgttgtttttttcccctccttctgagtaactactaatttctcttctttgtttgatatatttaaccattgattatatcttttttcctccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGAC

- -gttgttg
- - - - - - - - -cccctcc
- - - - - - - - - - - - ttctgag