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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGGTGCAACCTCAAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT

Basic information

species Glycine max
transcript GLYMA17G13440.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 10
------------gtaagtgacataccatgcgaactt---aatctcaattgattgatccttaaaatatgataa--ataagta---------tgtattg--tgtcatgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGGTGCAACCTCAAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT
             |    |||||  | |||    ||   ||||  |||   ||   ||||    | || ||   || ||||         | ||||   |||||||    | || ||||||||||| |||||||||||  |||||||||||||||||||||| || ||||| || |||||||| ||||||||||||||  | ||||| ||| | |||
gtgagtgatatcattgaagacatttc-tgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgt-ttttcagCCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGGTGCGACTTCAAGGGAAAGTATCAAAGCTGTTCTCAAGCTACCTCGCCTT
















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|21256128|gb|BQ453016.1|BQ453016
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|151400815|gb|EV270629.1|EV270629
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|31469021|gb|CD411049.1|CD411049
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|193703915|gb|FK634803.1|FK634803
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|23728320|gb|BU762211.1|BU762211
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|13481209|gb|BG510552.1|BG510552
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|26058441|gb|CA801355.1|CA801355
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|10843331|gb|BF066634.1|BF066634
EST:     GAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: GAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|21602499|gb|BQ612830.1|BQ612830
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|19347043|gb|BM891931.1|BM891931
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|207825151|gb|GD795056.1|GD795056
EST:     AAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: AAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|151400202|gb|EV270016.1|EV270016
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|23728843|gb|BU762488.1|BU762488
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|18039009|gb|BM307303.1|BM307303
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|207847382|gb|GD820423.1|GD820423
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|10848324|gb|BF070835.1|BF070835
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|22933543|gb|BU550682.1|BU550682
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|51334885|gb|CO978751.1|CO978751
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|15000364|gb|BI321178.1|BI321178
EST:     CCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: CCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|208298173|gb|GE091064.1|GE091064
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|208051460|gb|GD845927.1|GD845927
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|14011042|gb|BG725964.1|BG725964
EST:     GGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: GGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGGTGCAACCTCAAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT
 gattgat  putative branch site (score: 4)
         ttaaaatatgataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGGTGCAACCTCAAGGGAGAGTATCAAAGCTGTAATGAAGCTTCCTAGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC