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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcctctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

Basic information

species Glycine max
transcript GLYMA05G02190.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcc-tctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC
| ||   |     |   |    ||   |  ||      |   ||  |||  ||| | || ||  |  |     ||  |  |   | || ||  | ||  |||| |||||||| || || ||||| |||||||| ||||| ||||| |||||||||||| | ||||| || ||||||||||| ||||| ||||| || ||||
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccaga-atctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC

upper sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagtt--atcagacaacagatattagaaagctgaaatcctctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC
 | | | | |  |     |    |        ||   ||   |   || ||  |||||  || | |  | |    | | |  |    |  || || |||||||| |||||||| || || ||||| || ||||||||||| ||||| |||||||||||| | ||||| || ||||||||||| ||||| ||||| || || |
atttga-acattatgtggttgctttgtgctgcatcaaataaatgagcaattttatcagtgaatatagctgacttggtt-acttgtattgtttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC

upper sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 5
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcctctcattattt----tgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC
    |||  ||   ||       |   |   |             | ||  ||    ||    ||||         |  | | |   ||| |||    || ||||| |||||||| || || ||||| || ||||||||||| ||||| |||||||| ||  | ||||| || |||||||| || ||||| ||||| || || |
----aagttaatgtaactgggtttggtttggtgcacccagataaatgagcaatttaccagtgaatatagttgtctcggtaactttgtattgtttgttctgctagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAAACGCTTATTGCAGGTGGTCCTTTCGTGCTTCCCCTTGCACACAAAC

upper sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 5
----gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcctctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC
      ||      |   |  |   |      ||  || | ||  |     | | |  |||  ||||    |  |||  |       | ||  | |||  |||||| ||||| || || ||||||||||||||||||||||| || ||||||||||||||  | |||||||| ||||||||||| ||||||||||| || ||||
tccttgattttcttattaaggacttaaatgtaaataattggataagaaactaatca--agatgacagtc--tgaaaattttcttctgtgtctgtttttcattagCCTACAGTGGCTGCAATAGAAGCAGGGAAAGACATAGCCTTAGCCAACAAAGAGACCCTAATTGCTGGGGGTCCTTTTGTCCTTCCTCTTGCACACAAGC

upper sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcctctcattattttgtt--agCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC
|| ||     |   | |   |   | ||||||  |  |    || ||||| |   || |||   |    ||    |   |        ||  ||||||  |||| |||||||| || || ||||| || ||||| || || ||||||||||||||||| ||||||||||||||||| | |||  | ||||| ||| ||||||
gtctatttctaagtacaggtctacatctaaat-cgacaaatattatcagt-aggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC

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|254347803|gb|GR854052.1|GR854052
EST:     CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAG                         CCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
genomic: CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAGgtaaacctct ... attttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
EST: gi|254343989|gb|GR857745.1|GR857745
EST:     CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAG                         CCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
genomic: CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAGgtaaacctct ... attttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
EST: gi|9259629|gb|BE347776.1|BE347776
EST:     CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAG                         CCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
genomic: CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAGgtaaacctct ... attttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
EST: gi|10846631|gb|BF069467.1|BF069467
EST:     CAGATGCAGTTAGTGTAGTCACAGGAATAGTATGCTGTGCAGGACTGAAG                         CCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGGTTTGGCCAACAAA
genomic: CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAGgtaaacctct ... attttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
EST: gi|209718278|gb|BW657870.1|BW657870
EST:     CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAG                         CCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
genomic: CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAGgtaaacctct ... attttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA
EST: gi|192333074|gb|FK026403.1|FK026403
EST:     CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAG                         CCAACAGTTGCAGCGATAGAAGCAGG-AAAGACATAGCTTTGGCCAACAA-
genomic: CAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAGgtaaacctct ... attttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagttatcagacaacagatattagaaagctgaaatcctctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC
                                   tcctctcattatttt  CT-rich tract
                                        tcattattttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcctctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - aagaaaa
- - - - - - - - - -ccactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctgaa