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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaaccatttttttctttttaaatttagataaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG

Basic information

species Glycine max
transcript GLYMA01G37480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
----gttaaccatttttttctttttaa-atttagataaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG
     |     |||||| ||    ||  || |   |  ||  || |     |   | |||      | |     | | ||  ||| |   |||| |    |||||||||||||||||| || ||||| || |||||||| ||||||||| | || ||||||||  | || ||| | ||||||||| |  |||||
tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaat-ttgaccgcagatatattgtttactgttgtttcacttgtc----tgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
-gt-taaccatttttttctttttaaatttagataaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG-----------
 ||   || | |  ||  |  || |  ||    |  ||  |  ||   |||   |     |  | |  |    | ||  |||||           | | |||||||| ||||||| || |||||||| |||||||| || ||||||||||| ||||| ||  | || ||||| || |||||  |   ||||           
tgtacgactaatccttgatagttgacatttctaatcagttttttt--tttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 5
-gt-taaccatttttttctttttaaatttagataaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG
 ||   || | |  ||  |  || |  ||    |  ||  |  ||   |||   |     |  | |  |    | ||  |||||           | | |||||||| ||||||| || |||||||| |||||||| || ||||||||||| ||||| ||  | || ||||| || |||||  |   ||||
tgtacgactaatccttgatagttgacatttctaatcagttttttt--tttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAG

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
gttaaccatttttttctttttaaatttagataaaagcatgat---tgac-ttggtgttggtttttg-gtggtgagctgacatttgatgtgc---ttga--catca--tgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG-----------
            |||   | |||  | |||  ||  | ||||   |||| |     ||  |||||  |   |||     |  ||   ||     ||||  ||| |  | |||||||||||||||| || |||||||| || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||           
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
gttaaccatttttttctttttaaatttagataaaagcatgat---tgac-ttggtgttggtttttg-gtggtgagctgacatttgatgtg---cttga--catca--tgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG
            |||   | |||  | |||  ||  | ||||   |||| |     ||  |||||  |   |||     |  ||   ||     ||||  ||| |  | |||||||||||||||| || |||||||| || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
gtta-accatttttttctttttaaatttaga-taaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG
|||| |  |  |  |     ||| |    |  | |    | ||   | |   | | || || ||    | |  | |||     | |  ||  | |  || ||||||  ||||||| |||||||| || || |||||||| |||||  |||||||||| || ||||||||||| ||||| ||  ||  ||||
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccat-taggattatgcgcttaatataacacactctctaattc-ctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG

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|209697785|gb|BW663924.1|BW663924
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|31469425|gb|CD411453.1|CD411453
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGTCATATTTGTTCAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|15664810|gb|BI702173.1|BI702173
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|10844680|gb|BF067906.1|BF067906
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATTGGGCCCCCTGCAATGACAGTTAGTTCTATCTG
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCA-T-GGTCCCCTGCGATGACAGTTAGTTCTATCTG
EST: gi|9204241|gb|BE330465.1|BE330465
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCACATTTGTTTAG                         ATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|20813348|gb|BQ297826.1|BQ297826
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|37994961|gb|CF806550.1|CF806550
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|209703743|gb|BW656876.1|BW656876
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|20813177|gb|BQ297655.1|BQ297655
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|209697863|gb|BW663925.1|BW663925
EST:     TATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|27445947|gb|CA953070.1|CA953070
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
EST: gi|37996938|gb|CF808527.1|CF808527
EST:     TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAG                         ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA
genomic: TCCGGCTCCGCTGCATCCCCATATCTACAGTAACGGCCATATTTGTTTAGgtatgtatat ... catcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG
                              atttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaccatttttttctttttaaatttagataaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - -agataaaa
- - - - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - -gtgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttga