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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggttttgcttgtttactacattgctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 13
------gtctgg-ttttgcttgttt-actacatt---gctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
       | |||  |       ||| | | ||||   |||||      |  ||| |    | || |||  || | | |    || ||||| ||||| || ||||| ||||| |||||||||||||| |||||||| || || ||||| || || || || |||||||| |||
gtaaacatttggactccatacatttgatttcatttaagctatggcaaatacttacagtggagctcatttatgctgtttcatgttacagCTTTATGCCAACTATGCAATTGGGAAGGATGTCCAGGCCATGAAAGCCGTTGTGGGAGAGGAGGCGCTCTCTTCTGAGGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 12
gt-ctggttttgcttgtttactacattgctattttttctg-tttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
|| |   || ||  |   ||   | ||| | |      || | | ||||     ||         |  ||||| ||||||| ||||| || ||||| |||||||||||||| ||||| ||||| ||||| || ||||| || ||||| || |||||||| |||
gtacctattatgagtccatag-gctttgttttcagacatgatgtgtaagatgaattgacatctactgttttctgttcagCTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
------------------gtctggttttgcttgtttactacattgctattttttctgtttataagccatctt--------attgg----tgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
                     |  ||||| |     | | ||| |   ||  | |  || | |    || |         ||||     || | | ||   |||||||| ||||| || || || |||||||||||||| ||||| ||||| || || || ||||| || ||||| || |||||||| |||
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------------gtctggttttgcttgttta---ctacattgctattttttctgtttataagccatcttattggtgttttgtt-tcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
                                    |    | |||| || | ||    |   |||  |  |||| |      |    | ||| ||  | | || || |  |||||| | ||||| ||||| || ||||||||||| || ||||| |||||||| ||||| ||||||||||| ||||| || ||||| |||
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
gtctggttttgcttgtttactacattgctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
||    |||    |     || | ||    || | | ||   |    ||| || ||  | | ||  | |  ||||||||||||||||||||||| ||||| |||||||| || ||||||||||||||||| ||||||||||||||||| |||||||| |||
gtagtatttgatgttcgggctgcgttcaccttctctttgagcacgtcccaactaat--gcgattcttcttctttcagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------gtctggttttgcttgtttactac--attgctattttttctgtttataagccatctta--ttggtgttttgtttcttt---tcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
                |     | |    ||  || | |  ||| | |  |      |  ||| |  |  |     |    |  |||||   |    ||| | ||||| ||||||||||||||||||||||| || |||||||| ||||| || ||||| |||||  | || || || || |||
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------gtctggtttt--gcttgtttactacattgct--attttttctgtttataagccatcttattggtgttttgttt---cttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
                 | |||   |   |||    | |    || |  | | |   ||  |  |  |  |    ||    |  ||| |   | || ||| | || ||||| ||||| |||||||||||||| || || ||||| |||||||| |||||||||||  | || || ||||| |||
cacatgagagcatcatttgtggccatcaacttccccatttttctgatgaagtctgcttgagtcaagactttgggtttaacatggtgtctacccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
gtctggttttgcttgtttactacattgctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
                    |       | | | | |  |   || ||| | |||    ||| |  |   ||| |||||||||||||| ||||||||||| || || || || || ||||||||||| || ||||||||||| || |||||||| || |||
-------------------gtgagcgattgtgtctac-atcattatgccgt-ttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 12
gtctggttttgcttgtttactacattgctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
                    |       | | | | |  |   || ||| | |||    ||| |  |   ||| ||||| |||||||| ||||||||||| || || || || || ||||||||||| || ||||||||||| || |||||||| || |||
-------------------gtgagcgattgtgtctac-atcattatgccgt-ttaacaatgtctactggttttgcagCTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

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|10253833|gb|BE821599.1|BE821599
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|27426282|gb|CA937802.1|CA937802
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCCGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|27426098|gb|CA937618.1|CA937618
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|9898667|gb|BE607635.1|BE607635
EST:     CACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|19053919|gb|BM732586.1|BM732586
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|20812032|gb|BQ296510.1|BQ296510
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|16277795|gb|BI942566.1|BI942566
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCCGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|21255992|gb|BQ452880.1|BQ452880
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|7235272|gb|AW570601.1|AW570601
EST:     GAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: GAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|193391746|gb|FK354237.1|FK354237
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|16277730|gb|BI942533.1|BI942533
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|9258589|gb|BE346736.1|BE346736
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
EST: gi|16284553|gb|BI946150.1|BI946150
EST:     CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG                         CTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG
genomic: CCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAGgtctggtttt ... ttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
                                     tgttttgtttcttttc  CT-rich tract
      tattttttctgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggttttgcttgtttactacattgctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC