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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaattcaacatgaactagaggacactatcacatattaaacattgtctgatgaccatgtagtttattgaacatgggtggtttcattgcatatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTTAAAGATGGACAACAACTTGACAAACTTGTAGGAGCCAACAAGCCAGAAC

Basic information

species Glycine max
transcript GLYMA09G40970.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40970.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G066612_T01 (Zea mays), 3'ss of exon 2
ttcaattcaacatgaactagaggacactatcacatattaaacattgtctgatgaccatgtagtttattgaacatgggtggtttcattgc-atatgt-tccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTTAAAGATGGACAACAACTTGACAAACTTGTAGGAGCCAACAAGCCAGAAC
|||| |||| ||| | || | | | || | | ||| ||| || | | | || |||| | | || | |||||||||||||| |||||||||||||| || || || || |||||||| || || | || || || | ||||| || || || || ||||| || || |
-tcaaatcaa-atggtattaagtatatttccatctcgataggtctgtgctgctttcatctaaccctattcattgcgttgttttcgtgactattcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC
















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|15201232|gb|BI424764.1|BI424764
EST:     AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
genomic: AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACTgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
EST: gi|193404233|gb|FK366567.1|FK366567
EST:     AGAAATACACATCTATGATGTTCTTGCTAGTTGATGTGGATGATCTAACT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
genomic: AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACTgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
EST: gi|15203337|gb|BI426105.1|BI426105
EST:     AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCCTCTTTCTT
genomic: AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACTgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
EST: gi|208188050|gb|GD986864.1|GD986864
EST:     TGGATGATCTTAACTT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCT
genomic: TGGATGATC-TAAC-Tgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCT
EST: gi|13479405|gb|BG508748.1|BG508748
EST:     AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
genomic: AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACTgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
EST: gi|7478449|gb|AW666269.1|AW666269
EST:     AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTATCTT
genomic: AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACTgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
EST: gi|21257008|gb|BQ453896.1|BQ453896
EST:     AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
genomic: AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACTgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
EST: gi|13790090|gb|BG652681.1|BG652681
EST:     AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACT                         GACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT
genomic: AGAAATACACATCTATGATGTTCTTGTTAGTTGATGTGGATGATCTAACTgtaagtactg ... tatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgatgaccatgtagtttattgaacatgggtggtttcattgcatatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTTAAAGATGGACAACAACTTGACAAACTTGTAGGAGCCAACAAGCCAGAAC
 gtctgat  putative branch site (score: 4)
 tagtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaattcaacatgaactagaggacactatcacatattaaacattgtctgatgaccatgtagtttattgaacatgggtggtttcattgcatatgttccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTTAAAGATGGACAACAACTTGACAAACTTGTAGGAGCCAACAAGCCAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- caattca
- - - - - catgaac
- - - - - - - - - - - - - - - - - - - - - - - tctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgggtgg