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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG

Basic information

species Glycine max
transcript GLYMA15G07480.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaat-ttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
           |   | ||   |  |||| ||   |  |||   ||   || |||  |   |   ||||  | |  | ||||| || ||| || || | |||||||| ||||||||||| ||||||||||||||| |||||||| ||
-----------gttgtgaatatacttgtgtttttgttatttctgcacacta-tttcttcttatatttgacatagtgtattgttacaatgt-atgtt-gcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG

upper sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 8
ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
                       | |||   |||  | ||         |   |||  || |    | | |    |||| ||  |   || | ||||||||||||| ||||| ||||| ||||||| ||| |||||| ||||||||
---------------------gtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagta-acatttattggacacttgt-tttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG

upper sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 7
ttcaatcctgcgcaatcaaacaaaatgtgcttgcata---ttttgatcattgtaatttggttacactcttg-attttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
 |      |    |||  | ||   | ||  | || |   |||| | | ||  || |   | | || || |  | |||   || || || ||      ||  || ||||| ||||||||||| ||||| ||||||||  |||||||||||
gttggatatattaaat-gagcattgt-tggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctg--ttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG

upper sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 7
ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaatttgttccattgttatat---ttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
        || |             ||||  |    ||   |  |||||  |  | ||  |   ||  ||||   |||   |  |||   || |   ||  |||||||| ||||||||||| ||||| |||||||||||||||||||| 
------gttgtgtgtatgtttctgctgtgtctattcat---gcacattgccacattgtaccctcctccatttcacattatgtttatttaaatgtgtattacagGACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT

upper sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G448715_T02 (Zea mays), 3'ss of exon 8
ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaatttgttccattgttatattt-gtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG---------
 | | |  |  | ||||  |  | ||    |||    | |  | |||     ||||  | ||   | |||    ||| | | |        | ||| |||||||||| ||||| ||||| ||||||| ||| |||||| ||||| ||         
gtaatttatttgaaatctcatcacattattttgtgcctct--accatatatctttgtatgca---tggataggtaatgtttactggcaacttgttttgtagGACTGATAGTGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACTTGGTAAATATA

upper sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 8
--ttcaatcctgcgcaatcaaacaaa-atgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
    ||  | |  |        ||   ||||   |   | | || ||  || | |  ||   |   |||    | |||      | ||   ||    ||  |||| ||| ||||||||||| ||||||||||||||| |||||||  ||
ccaccatccatatgtgtgtgtgcatgtatgtttgtatgtgtgtttatggtt-ttacctgacaattttctgttatctgatcacactacaacattt--cttacagGAATGAAAGTGCTTTGAAGTTTGGATGGTTTTTCATGTTTTATTTG

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|21994675|gb|BQ786203.1|BQ786203
EST:     ATTCCTGGAGCATATGTCTTGTGGTATCGCCCATTATATCGTGCTTTTAG                         GACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
genomic: ATTCCTGGAGCATATGTCTTGTGGTATCGCCCATTATATCGTGCTTTTAGgtaattattt ... atatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
EST: gi|10255229|gb|BE822995.1|BE822995
EST:     TGTGGTATCGCCCATTATATCGTGCTTTTAG                         GACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
genomic: TGTGGTATCGCCCATTATATCGTGCTTTTAGgtaattattt ... atatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
EST: gi|16343904|gb|BI969499.1|BI969499
EST:     ATTCCTGGAGCATATGTCTTGTGGTATCGCCCATTATATCGTGCTTTTAG                         GACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
genomic: ATTCCTGGAGCATATGTCTTGTGGTATCGCCCATTATATCGTGCTTTTAGgtaattattt ... atatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
EST: gi|254315478|gb|GR825287.1|GR825287
EST:     ATTCCTGGAGCATATGTCTTGTGGTATCGCCCATTATATCGTGCTTTTAG                         GACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCT
genomic: ATTCCTGGAGCATATGTCTTGTGGTATCGCCCATTATATCGTGCTTTTAGgtaattattt ... atatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtaatttggttacactcttgattttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
                  tcttgat  putative branch site (score: 4)
                                       attgttatatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG

- - atcctgc
- - - - - -gcaatca
- - - - - - - - - aacaaaa
- - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacactc