Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttgtttgttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttatattttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG

Basic information

species Glycine max
transcript GLYMA05G07020.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 5
gtacttttgtttgttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttatattttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG
|||  |    || |||||      | || | |     || |   | | | | || ||   | |    ||| |||    | || |||  |   || ||| |     ||||||| |||||  |||| || ||| || | ||||| ||||| ||||||||||||||||||||||||
gtagctcctgtttttgagt-----tgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtat-tagactattttcatatgtaaattgt-----agATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
gtacttttgtttgttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttata-ttttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG
                   ||   || | ||   | |     | ||   ||  | |||| | |||  |  |   || |||   ||      ||||| ||     |||||||||||| ||  |||||||||||||  | ||||| || || |||||||||||||||||||| |||
----------------gtaaactattactgttgttgtttatccctg---tacttttgaattgtgg--ggctaggactaaa-gtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G158479_T02 (Zea mays), 3'ss of exon 6
gtacttttgtttgttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttat--attttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG
                             |||||     |  ||||  | ||   || ||||| |||   |    |   |  |   |||| | |   || || |  ||||||||||| ||  | |||||||||||  | ||||| || || |||||||||||||||||||| |||
-----------------------------gtaaactaactgtcatgt-tgattcctgtacttttgaattgtggggcaggactaaagtttgatcactcatattccctcagATGGGTAAGGATGTCGTATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 6
-gtacttttgtttg--ttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttatattttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG
  || ||||  |    || |   ||     ||  ||   | ||  | |    ||    ||  ||||   ||  | ||  || ||||  |     |||  ||  | | |||||||||||||| |||||||||||| || | ||||| || ||||| || ||||||||||| ||||||
gttatttttcctccacttaaaatataagaacataaatctttatgccttatggtac---tgtcctttctcagtgtcat--gatataaact-----ttactttacggtgcagATGGGTAAAGATATTGTATCATTCTTGGCCTGGGCAGCTGAACCAGAAATGGAAGAGAGGAAACTG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 5
----gtacttttgtttgttgaggaatggttt-cagtaaatctcatcacat-ggattatctatgaactttggaagaattatacgaaat--aattttttggttat-----attttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG
    ||  |  | |   |     |||  ||| |||   ||    |   ||  ||||     |   || ||    |||||||  |  |  |||||||   || |     |   || | ||||||||||||||  ||||||| ||| || | ||||| || ||||| |||||||||||||| ||| ||
gttagttttcctctgcttaagaaaataatttgcagaccataaagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcagATGGGTAAAGATGTTGTATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG

upper sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 6
--gtacttttgtttgttg-aggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttatattttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG
  |   |||  | |  |  |        ||  ||   ||| |  ||    |||   | |    |||  | |  ||| |  |   | | | ||   || ||| || | |||||||| |||||  ||||||||||  |||| ||||| |||||||| ||||||||||| || ||||||
gtgggttttcatctactctaattgcaacttgggtgcttctta--actgtaattgcatct---ttttcaaggtgttagaaaattgagtgtcttccata-attctggtgcagATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTG

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|207789052|gb|GD762164.1|GD762164
EST:     ATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacttttgt ... tttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|21601541|gb|BQ611872.1|BQ611872
EST:     TGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: TGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacttttgt ... tttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|15285987|gb|BI469878.1|BI469878
EST:     ATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacttttgt ... tttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|16343642|gb|BI969237.1|BI969237
EST:     ATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacttttgt ... tttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|58018184|gb|CX704926.1|CX704926
EST:     ATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacttttgt ... tttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgaactttggaagaattatacgaaataattttttggttatattttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG
                                            ttttgct  CT-rich tract
             aagaattatacgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttgtttgttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttatattttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA