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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaatgtttcattattcttccctttgtatccatttgttctattttgtgacatactattattctttgtatgtgcacactaatgtgtttcatcttgcttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
gtactgaatgtttcattattcttccctttgtatccatttgttcta-ttttgtgacatactattattctttgtatgtgcacactaatgtgtttcatcttgc--ttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT
                           |   |       ||| ||  | | | |  |  | | ||| |||||| |       | || |   |  | |||   |  ||  |||||||| || ||||||||||||||||||||||| ||||||||  |  | || 
--------------------------gtaagagttgcaagttgtaactctttcagctgttttcattgtttgtaggatttgtttcatttaactatttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 11
gtactgaatgtttcattattcttccctttgtatccatttgttctattttgtgacatactattattctttgtatgtgcacactaatgtgtttcatcttgcttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT
         || |   ||| ||    ||| |||  | | |||||   |  ||  ||    |   |  ||   ||    || || |   |||| |     |  ||| |||||||||||||||||||| ||||||||||| ||  ||||||| ||| | || 
---------gtatgcatatgctgttttttttatttact-gttctgcgtcttg-tatgtcctaccttctttcctgacttcaatatttaatttccttgatttggttgcagTGGTGAAACTGAGGATACATTCATTGCTGATCTGGCAGTTGGTTTATCCACG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 3'ss of exon 14
gtactgaatgtttcattattcttccctttgtatccatttgttctattttgtgacatactattattctttgtatgtgcacactaatgtgtttcatcttgcttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT
        | |     ||| ||| ||| | | |     || |  |  | ||  |  ||||  |  | || | | |    |||  ||||||||||      |     |||||||| |||||||||||||||||||||||  |  | ||||| || || || 
-------gtatactgatatgcttacctgtctttattcctggtggacctggt--ctgactaccaaccatt-tgtatattgact--tgtgtttcat------tgccacagTGGTGAGACTGAGGATACCTTCATTGCTGATTTGGCTGTTGGTTTGGCCACG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 14
gtactgaatgtttcattattcttccctttgtatccatttgttctattttgtgacatactattattctttgtatgtgcacactaatgtgtttcatcttgcttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT
                ||        ||| | || | |   | | |||        | |||||||  |   |||     ||||||    ||   |||||  | |  |||||||||||||||||||| |||||||| ||||| |||||||| || || || 
---------------gtacaaaatgttttttgtctactaaatttttttc-------agtattatt--tgaaatggcattactaatccagtttcccttgcacaatacagTGGTGAAACTGAGGATACTTTCATTGCAGACCTTTCAGTTGGTTTGGCCACG

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|58014968|gb|CX701710.1|CX701710
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|254343119|gb|GR859281.1|GR859281
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|57574275|gb|CX547250.1|CX547250
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|254320423|gb|GR826872.1|GR826872
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|254335782|gb|GR847310.1|GR847310
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|58021375|gb|CX708116.1|CX708116
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|10254318|gb|BE822084.1|BE822084
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|16343634|gb|BI969229.1|BI969229
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|7588392|gb|AW704189.1|AW704189
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|254329397|gb|GR838950.1|GR838950
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|58020394|gb|CX707136.1|CX707136
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|213597412|gb|DB977775.1|DB977775
EST:     CATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTCTCGA-TAGCAA
genomic: CATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGT-TGGATTAGCAA
EST: gi|151408704|gb|EV278512.1|EV278512
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|254317871|gb|GR832039.1|GR832039
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
EST: gi|254329396|gb|GR838949.1|GR838949
EST:     GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAG                         TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC
genomic: GTGAGAATGTCTAAACAAGCTGGTTGGGGTGTCATGGCTAGCCACAGGAGgtactgaatg ... cttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catactattattctttgtatgtgcacactaatgtgtttcatcttgcttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT
                         cactaat  putative branch site (score: 2)
                                        tcttgctt  putative PPT
     tattattctttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgaatgtttcattattcttccctttgtatccatttgttctattttgtgacatactattattctttgtatgtgcacactaatgtgtttcatcttgcttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT