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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattgataaaacaagttagacttgcttatgtgattcttctctcctgatttttttttttttctcag

Basic information

species Glycine max
transcript GLYMA01G00430.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G00430.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 8
TCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaa------ttattgataaaacaagttag---acttgcttatg-----tgattcttctctcctgattt-----ttttttttttctcag-----------
||| ||| | |||||||| ||||  || |||||||| ||||| || |||||||  |||||||| ||||| || ||||| ||||| ||||||||||| || || |      | ||    |  || | | ||   | || |||  |     | | |  ||| |   ||| |       ||| || | ||||           
TCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcagtcatcagcattaccaataaggaaatttactttagaaggttaaattgtcttttgagatctaggatcctttgttctttcagcatctctaatt

upper sequence: GLYMA01G00430.1 (Glycine max), 5'ss of exon 11
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 5'ss of exon 10
TCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattgataaaacaagttagacttgcttatgtgattcttctctcctgatttttttt-----tttttctcag
||| ||| | ||||| || |||||||| ||||| ||||||||||| ||||||| |||||| || ||||| || ||||||||||| || ||||||||||||||||| | | ||   |||   |   ||| |     |  || |    |  | |||  ||||     |  |  ||||
TCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTGACTGCACCGCAGAAGGACTGAAAgtaat-aataatgcgacagagttacctttcaggatttcttttctggtggtaattagttttgtaattcctcttcag

upper sequence: GLYMA01G00430.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 11
TCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattgat---aaaacaagttagacttgcttatgtgattcttctctcctgatttttttttttttctcag-------------
|||| || | ||||| || |||||||||||||||||||||||||||||||| || |||||||||||||| || || |||||||| || |||||| |||| ||||| ||||||   |  | |||    | |||||| | |  ||||||  |  | | || ||||| | |||  |             
TCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAGACTGCACTGCGGAAGGATTGAAGgtaatgattgattgtagtaaaagcaccatttgcttcttt--ttcttcgttg-taacttctttttctctctttgttctttttcttag

upper sequence: GLYMA01G00430.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 5'ss of exon 10
TCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgta-----attattgataaaacaagttagacttgcttatgtgattcttctc-tcctgatttttttttttttctcag------------------------
| |     | ||||| ||||| ||||| ||||||||||||||||||||  |  |||| || |||||||| || ||||||||  |  |||||||  | || ||      |||   |         | |   |||  | |  || ||||  |  | ||||  || |   |  |   |                         
TATGGCCTACTGGTATCGTCATATTTCTAAAGGTGCTTGGCCTTTTTCTTCAAGAGACCACGGATGGCCTATCTCTGACTGTTCGTCTGAAGGCTTAAAGgtgtgttgattcccgtgtgtgtgcgcttttctttttaaaatgtttctgatgatgctgagcttctgcgtacttgtaaaaaattaatgtaactgtggctctt

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|12773845|gb|BG238772.1|BG238772
EST:     CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAA                         GCTGTTCTATTACTATCCAAAATTGCACCACAAATAGTTGGTGAGCC
genomic: CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattg ... tttttctcagGCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCC
EST: gi|18733901|gb|BM527876.1|BM527876
EST:     CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAA                         GCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
genomic: CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattg ... tttttctcagGCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
EST: gi|22524821|gb|BU083632.1|BU083632
EST:     CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAA                         GCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
genomic: CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattg ... tttttctcagGCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
EST: gi|18732433|gb|BM527041.1|BM527041
EST:     CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAA                         GCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
genomic: CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattg ... tttttctcagGCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
EST: gi|19269470|gb|BM885726.1|BM885726
EST:     CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAA                         GCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
genomic: CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattg ... tttttctcagGCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
EST: gi|213590932|gb|DB973729.1|DB973729
EST:     CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAA                         GCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
genomic: CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattg ... tttttctcagGCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
EST: gi|24136389|gb|BU926899.1|BU926899
EST:     CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAA                         GCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA
genomic: CTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattg ... tttttctcagGCTGTTCTATTACTATCCAAAATTGCACCAGAAATAGTTGGTGAGCCAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTGACTGCACAGCTGAAGGACTGAAAgtaattattgataaaacaagttagacttgcttatgtgattcttctctcctgatttttttttttttctcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG