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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catattaatatgatctagtagttgatgactgtaattcaaataaatttttattgttgattatataatgattcataattaatgtcttctcttttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCATGGAGTTGGAAGTGTTTTTCATGCTGATCCTGTTATTCTTCACTATA

Basic information

species Glycine max
transcript GLYMA01G39200.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G101438_T03 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------------catattaatatgatctagtagttg-atgactgtaattcaaataaatttttattgttgattatataatgat------tcataattaatgtcttc------tcttttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCATGGAGTTGGAAGTGTTTTTCATGCTGATCCTGTTATTCTTCACTATA--
                                                                         | ||| |  | ||| |  || || ||     |||||   ||   |      | | |     | || ||       |   || || | |  |       | |  |||||| || ||||||||||| || |     | |||||| ||  ||||||||||||||||||| ||||| |  |||||||||||||| |||||| | ||||| |  |  
gtatgtaatttctgagtaaccaagcttttaaacagatgcacatatttttttattatctttatcttaaaaaacaacattcagtttatcgataagctgtattgtcttaatttgtatgcgtaacagatctggtaatcaaaacgaactcttgttccaactactatacttacgacatttaatctttgaagGGATCATGCAGACAAGTTCAAGTTTGGTGTAGTTAGACAGTTTGTTGGCCATGGGGTTGGCAAAGTTTTTCATGCTGAGCCTGTTGTGCTTCATTTCAGT

upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------------catattaatatgatctagtagttg-atgactgtaattcaaataaatttttattgttgattatataatgat------tcataattaatgtcttc------tcttttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCATGGAGTTGGAAGTGTTTTTCATGCTGATCCTGTTATTCTTCACTATA
                                                                         | ||| |  | ||| |  || || ||     |||||   ||   |      | | |     | || ||       |   || || | |  |       | |  |||||| || ||||||||||| || |     | |||||| ||  ||||||||||||||||||| ||||| |  |||||||||||||| |||||| | ||||| |  |
gtatgtaatttctgagtaaccaagcttttaaacagatgcacatatttttttattatctttatcttaaaaaacaacattcagtttatcgataagctgtattgtcttaatttgtatgcgtaacagatctggtaatcaaaacgaactcttgttccaactactatacttacgacatttaatctttgaagGGATCATGCAGACAAGTTCAAGTTTGGTGTAGTTAGACAGTTTGTTGGCCATGGGGTTGGCAAAGTTTTTCATGCTGAGCCTGTTGTGCTTCATTTCA

upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 3'ss of exon 7
catattaatatgatctagtagttgatgactgtaattcaaataaatttttattgttgatt--atataatgattcataattaatgtcttctcttttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCATGGAGTTGGAAGTGTTTTTCATGCTGATCCTGTTATTCTTCACTATA
   |  |  |  | ||   || |      || |||  | || ||| |||  |     ||  ||    |  ||  |  |||   |      | |  |||| ||||| |||||||||||| |||||||||||||||| |||  ||||||||| |||||||||||| ||||||||||||| ||||| ||||| || ||||| |
-gcagcatcaataacttacagcttgcatatg-aatatatatgaatgtttggttccagtttaattcttttttttttttttacaattaatgttctcttttgaagTGACCATGCAGATAAACATCGTTATGGTGTTGTGCGAATGTTTGTTGGGCATGGAGTTGGACGTGTTTTTCATGCCGATCCAGTTATCCTACACTACA

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|213604191|gb|DB978715.1|DB978715
EST:     TCAATATGTGCACCAAGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCA                         TGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
genomic: TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
EST: gi|51336069|gb|CO979935.1|CO979935
EST:     TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCA                         TGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
genomic: TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
EST: gi|31459515|gb|CD401543.1|CD401543
EST:     AAAACAATTCA                         TGATCATGCAGATAAAGATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
genomic: AAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
EST: gi|31462284|gb|CD404312.1|CD404312
EST:     GGAGTTCAAGAAAATTGGCAAAACAATTCA                         TGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
genomic: GGAGTTCAAGAAAATTGGCAAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
EST: gi|51345228|gb|CO985961.1|CO985961
EST:     TCAATATGTGCACCAGGAGTGGAGTTCANNANTATTGGCAAAACAATTCA                         TGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
genomic: TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
EST: gi|209710615|gb|BW676541.1|BW676541
EST:     TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCA                         TGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
genomic: TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
EST: gi|192300116|gb|FG991892.1|FG991892
EST:     TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAA-CAATTCA                         TGATCATGCAGATAA-TATCGTTATGGTGTTGTCCGACAGTTTGTGGGC-A
genomic: TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
EST: gi|51335002|gb|CO978868.1|CO978868
EST:     TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCA                         TGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA
genomic: TCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCAgtaagatgtc ... ttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattgttgattatataatgattcataattaatgtcttctcttttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCATGGAGTTGGAAGTGTTTTTCATGCTGATCCTGTTATTCTTCACTATA
                            aattaat  putative branch site (score: 3)
                              ttaatgtcttctcttt  CT-rich tract
     ttgttgattatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catattaatatgatctagtagttgatgactgtaattcaaataaatttttattgttgattatataatgattcataattaatgtcttctcttttctttgtagTGATCATGCAGATAAATATCGTTATGGTGTTGTCCGACAGTTTGTTGGCCATGGAGTTGGAAGTGTTTTTCATGCTGATCCTGTTATTCTTCACTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - tgatgac
- - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat