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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtttatctatctttcttgatccattgtttaaaataccagattaggatggtactattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG

Basic information

species Glycine max
transcript GLYMA03G03250.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G03250.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g29990.1 (Oryza sativa), 3'ss of exon 11
---cgtttatctatctttcttgatccattgtttaaaataccagattaggatggtactattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG
     |||  || | | |    || ||  ||  | | | ||   | |      || |  || ||| |||   |  |  || |   ||   |     |    |||||| |||||||||||||||||||||||||| |||      || |||| |||   ||||||| |||  || || ||||| ||  |   |
ttatttttgactgtttcttcc-atacagggtacagatt-cctcctaattcccttagttattcttaagcagtttg-cacataattctggcatcttcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG

upper sequence: GLYMA03G03250.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g19140.1 (Oryza sativa), 3'ss of exon 8
cgttt--atctatcttt--cttgatccattgtttaaaataccagattaggatggtactattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG
| |||  |  ||| |||  ||   ||    ||  | | ||| |||||    |  || |  || ||| ||||  |  |  || |   ||   |     |    |||||| |||||||||||||||||||||||||| |||      || |||| |||   ||||||| |||  || || ||||| || ||   |
catttgaacttatttttgactgcttcttccgtacagagtac-agattcc--tcctaattattcttaagcaatttg-cacataattctggcatatgcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATTTGCAG

upper sequence: GLYMA03G03250.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G420055_T01 (Zea mays), 3'ss of exon 8
---cgtttatc-tatctttcttgatccattgtttaaaataccagattaggatggtactattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG
      ||||  || ||||||| | | || || |  | |    |  ||     | | || |    ||  ||    |  || ||  |||||    | ||| |||||||| ||||||||||||||||| |||||||| ||       || || | |||    || ||| |||| || ||  |||| ||  |   |
acctaattatggtagctttcttta-caatagtctttattctttgtataattctg-agtaatgaacatataatcagttatactatgttgctgc--atctgcatagGTGTCATGATTGCTTGGACTGGGATTGAGCATTTTGTTGCCGGGAGGTTTGAGGACCCACCTGCTGCTGATGAGTCTGATGATATGCAG

upper sequence: GLYMA03G03250.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0048g00390.t01 (Vitis vinifera), 3'ss of exon 11
cgtttatctatctttcttgatccattgtttaaaat-accagattaggatggt-actattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG
  | |   |||        |    |  || | | |  | | |    | | ||  |   |       ||    |  |||| | ||| |  || |  ||| ||||||| ||| | |||||||||||  | |||||||| ||||||||||||||||| ||||| || |||||  | ||||||||||| | ||||
-atgtgaatattacatacaaggggtaattaatatttgctaaaaagagttagtcgcccatgacctctcattgaagattatga-ctttccattcatttgactagGTGTTATGGTGGCTTGGACTGGCTTGGAGCACTTTCGCATGGGAAGATATGATCCTCCACCACCTGCTAATGAACCTGAAGATTATGTG

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|16345087|gb|BI970682.1|BI970682
EST:     GAATGGCCTGCAACTTGTATGCCCACCTCCTCGGCTCTGTACTGATAATG                         GTGTAATGA-TGNTTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATAT
genomic: GAATGGCCTGCAACTTGTATGCCCACCTCCTCGGCTCTGTACTGATAATGgtaatcatat ... aactgaatagGTGTAATGATTG-CTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATAT
EST: gi|51336111|gb|CO979977.1|CO979977
EST:     GAATGGCCTGCAACTTGTATGCCCANNNNNNNGGCTCTGTACTGATAATG                         GTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATG
genomic: GAATGGCCTGCAACTTGTATGCCCACCTCCTCGGCTCTGTACTGATAATGgtaatcatat ... aactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATG
EST: gi|17153766|gb|BM143699.1|BM143699
EST:     GAATGGCCTGCAACTTGTATGCCCACCTCCTCGGCTCTGTACTGATAATG                         GTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATG
genomic: GAATGGCCTGCAACTTGTATGCCCACCTCCTCGGCTCTGTACTGATAATGgtaatcatat ... aactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggtactattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG
     tactattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtttatctatctttcttgatccattgtttaaaataccagattaggatggtactattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - aaaatacc
- - - - - - - - - - - - - - - - - - - - - - -gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgct