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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattattttttccttgtgttttgcttaccattgactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCATAGCAACCATCAGGGTTCCAGCTTGAT

Basic information

species Glycine max
transcript GLYMA10G00490.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 8
gtaagattattttttccttgtgttttgcttaccat-tgactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCATAGCAACCATCAGGGTTCCAGCTTGAT--
|||||   || | ||     |||| ||||||   |     | || || |  ||| || |  |    |  ||    |||    || | |||||||||||| || || || ||||| |||||||| |||||||| ||||| |||||||| || || || ||||| |  |    | || |   |||   |||     
gtaaggc-atctgttga--atgttctgcttattttgctttttaacttctccctggaacttgttccataaaacagcgttc-ttgtcg-tgcagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATGCTGTCTTACTCGTGTAAGGACGCAATG-CTAT-ACACTTCATTCTTCTCGT

upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 8
gtaagattattttttccttgtgttttgcttaccattgactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCATAGCAACCATCAGGGTTCCAGCTTGAT
|| |||  | |||  |    |  ||  |||     | |    |  || |       |  ||       |   ||| |||     | |||||| ||||| ||||| || ||||| ||||| || |||||||| ||||| |||||||||||||| || ||    |||||  |   |  |  |       ||| 
gtgaga--aatttgccagctttcttctcttcttgctcaacctaccttgagtccttttcaataaaccaaa---ttgcttgt----gttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAATGATGGGTGTATCAATGCTGTTTTGCTAGTGTAGAACCATAGTGAGATTTTGTTTATGGTGATGAA

upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 8
--gtaagattattttttccttgtgttttgcttaccattgactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCATAGCAACCATCAGGGTTCCAGCTTGAT
  |  | ||         ||| |||  |  ||       ||  |    || ||     |  || |    ||||||  | ||       |||||| ||||| ||||| || ||||| ||||| || || ||||| ||||| |||||||||||||| || ||  | |||||  |   |  |          ||| 
gtgagaaatctgccaactcttctgtgctctttttacccaaccta--ccttgaccctgttcaat-taacagaatttcttgtgt------tgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATGCTGTTTTGCTAGTGTAGAGCCATAGTGAGATTTTGTTGATGGTGGTGAA

upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagattattttttccttgtgttttgcttaccattgactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCATAGCAACCATCAGGGTTCCAGCTTGAT
||||| | |   | | |      || |   |      |||  |||||| | |    |    || ||     | | ||     ||  | |||| ||||||||||| || ||||| || ||||| || || || ||||||||||||||||| ||||| |||    ||  |   ||     ||   ||  ||  
gtaag-tgacaatatacacaaccttagtgca-----aactataattttgatt----tcagagtcttaactctctcttcaatttgacttcagGAAAATACGCTCAAGTGACAAACAATCCAGAGAACGACGGATGTATAAATGCTGTTTTACTTGTGTAACCAAATGTCCGGCACTGTCGTAGAAGTATGGA

upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
gtaaga--ttattttttccttgtgttttgcttaccattgactgaa-attttaactgaaa--ttgatgtgttggaattttg----tttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCAT-AGCAAC--CATCAGGGTTCCAGCTTGAT
||||||  || |||  |  ||||  | |  | |   ||   ||     || | ||| |   ||  | | ||  | ||||     | ||  ||||||| ||| |||||||| || || |||||||||||||| |||||||| ||||||||||||||||||||||| ||||   || | ||||  || || |  |   |      
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG---

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|192333081|gb|FK026410.1|FK026410
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|17963424|gb|BM270173.1|BM270173
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|17400258|gb|BM177032.1|BM177032
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAAC
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAAC
EST: gi|26043857|gb|CA782197.1|CA782197
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|31459134|gb|CD401162.1|CD401162
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|209725840|gb|BW654703.1|BW654703
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGT-GTGTGGG                         GTAA-TACGCTCAGGTCACA
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACA
EST: gi|22932705|gb|BU549844.1|BU549844
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|192329668|gb|FK022934.1|FK022934
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
EST: gi|209725841|gb|BW654704.1|BW654704
EST:     GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGG                         GTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG
genomic: GAATGTCAGTGAACTTGGTCTTGTCACACCTGCTGGGAAAGTTGTGTGGGgtaagattat ... gtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCATAGCAACCATCAGGGTTCCAGCTTGAT
     aaattttaactgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattattttttccttgtgttttgcttaccattgactgaaattttaactgaaattgatgtgttggaattttgtttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCATAGCAACCATCAGGGTTCCAGCTTGAT

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