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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccatttttttgtgcagtgataattttgaaggcattttatcaacttcattcttttatataccaattgagcag

Basic information

species Glycine max
transcript GLYMA05G28950.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 16
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 5'ss of exon 14
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccatttttttgtgcagtgataat-tttgaaggcattttatcaacttcattcttttatataccaattgagcag
||||  || |||||| | ||||||||||| || || || ||||| ||||||||| |||||||||| ||||||||| ||||| | |||||         ||||  || | | ||   |  ||   ||||| | |  | |||| |      ||||  | ||   | | | ||               
GGAAAAGATAAGACTGCTGAAGAGAGAAGGATAGCTATCTGTATATTTGATGATATTGCAGAGCAATGTCGTGAATCTGCTCTCAAgta---------tgttcctcaaagctatt-tggttggatgcagggcttgtatttgtaactgaattatgtattttcctatctgattag------------

upper sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 16
lower sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 13
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccatttttttgtgcagtgataattttgaaggcattttatcaacttcattcttttatataccaattgagcag
|  | |||||| ||   ||| ||  |||| ||||| || || ||||||||||||||||||||||| ||||| ||||| ||||| | ||||    |   ||    | |   | ||| |||| |||       || ||| |     | ||| || ||    | | | |   ||      |   |||
GCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAGgtaacagtttaatgacccttt---taacctttttattggatga-aatgattcttctaacttttgatgaaacgtaatttgtatgatctgtggttctcag

upper sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G033619_T01 (Zea mays), 5'ss of exon 13
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccattt-ttttgtgcag-tgata-attttgaaggcattttatcaactt-cattcttttatataccaattgagcag---
|| | | | ||  | |||||||| ||||| ||||| || || ||||||||||||||||| ||||| || |||||||| || |||| ||||    | |  | |    ||  | ||  |||  || ||| || ||| | ||| |   |   | | ||||  || |||  |||| | |   |  |||       
GGTAAGAATAAATCACCAGAAGAAAGAAGGATTGCCATATGCATTTTTGATGATGTTGCTGAGCATTGCCGTGAAGCAGCAGTTAGgtaacagttgtacgatcca-tacatgacactttgcttggtgaaggtgaaagattgttgtgagctgtgatcattttacatgtttttttgtgatatctgattgtcag

upper sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 16
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 14
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccatttttttgtgcagtgataattttgaaggcattttatcaacttcattcttttatataccaattgagcag
||||| || || ||  | ||||||||||| ||||| || || |||||||||||||| ||||| || || |||||||||||  ||||||||| |  |     |   || | | |   |   |||||    |   | ||||  ||   |  ||   ||  | |   ||| | |  ||         
GGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAgtaaggatacgc--atccactggatcattttacatttgtaggtttccagttttagagttctgataa-gacaccttatatttgtttggcag--------

upper sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 5'ss of exon 14
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccatttttttgtgcagtgataattttgaaggcattttatcaacttcattcttttatataccaattgagcag
|| |  || || ||  | ||||||||||| |||||||| || || |||||||||||||||||||| ||||||||||| ||| |||||||||     | |     |     ||    ||| |   |   ||   | |||||  |   |||   | |  | ||| || || ||     | || |||
GGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAAgtaagtgaa-tatacccctaggacttttactttgtaattttggttgcagttttg--gctgtttatgcgatgtaattgttctaaatgtggttggaacag

upper sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 16
lower sequence: PP1S207_33V6.1 (Physcomitrella patens), 5'ss of exon 14
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttcta--ggttaccatttttttgtgcagtgataattttgaaggcattttatcaacttcattcttttatataccaattgagcag----
||||  ||    || || || || |||||| |||| || ||| |||| ||||||||||| ||||| ||| | || |||||| ||||||||||| | | | ||  |  |  | ||   |   |  |  ||| |    | ||   |   | |  ||  || ||      | |   |   ||||||       
GGAAAAGAACGAACACCTGATGAAAGAAGAGTTGCCATCTGTGTTTTCGATGATGTTGCCGAGCAATGTGGCGACGCTGCTATTAAgtaagcattttattttagtgcattgattgtaagactcat-cgca-ttcccacttgagacatactggatatacatcgaaagctgagcca--gattgagtttaaag

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|21677277|gb|BQ629628.1|BQ629628
EST:     ATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAA                         GTATTATGATACCTATCTCCCATTCCTGTTGGAGGCTTGTAATGATGAGAC
genomic: ATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactc ... aattgagcagGTATTATGATACCTATCTCCCATTCCTGTTGGAGGCTTGTAATGATGAGAC
EST: gi|21887848|gb|BQ741061.1|BQ741061
EST:     ATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAA                         GTATTATGATACCTATCTCCCATTC
genomic: ATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactc ... aattgagcagGTATTATGATACCTATCTCCCATTC
EST: gi|17153820|gb|BM143753.1|BM143753
EST:     ATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAA                         GTATTATGATACCTATCTCCCATTCCTGTTGGAGGCTTGTAATGAT
genomic: ATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactc ... aattgagcagGTATTATGATACCTATCTCCCATTCCTGTTGGAGGCTTGTAATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAAgtaagcactctttgtttttctaggttaccatttttttgtgcagtgataattttgaaggcattttatcaacttcattcttttatataccaattgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT