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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaggctcaagttcgctcgtttgatgtctttaacacttgcatatagatcacattatggataggcttggcttgtaacattgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA

Basic information

species Arabidopsis thaliana
transcript AT5G59960.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59960.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g05830.1 (Oryza sativa), 3'ss of exon 10
aacaggctcaagttcgct--cgtttg--atgtctttaacacttgcatatagatcacattatggataggcttggcttgtaacattgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA
    |   ||  ||| |    | |||  ||| || |   | ||| | ||  ||   | ||    | |  ||   |  |||  |||   |  | | |   | |||||||| || || || |||||| | || || || || ||  |||| || ||||||||||||||||| ||||| |||||||||||| |  |  ||||| | |
--ttgatccattttcacagagggttgccatgactattctatttgaa-attaatgtgaatacttgttgagttatataataattttgactta-tgtcgcgctacagGTTGGCCGATATCCAAGGCATGTGATAAGCCTGTTCTTTCGGCTTCTCTATCCGTGGTACTGGCCTTCCTCTTGCTGGAACTTTATTATGACTTGCGTCA

upper sequence: AT5G59960.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM5G871336_T01 (Zea mays), 3'ss of exon 10
------aacaggctcaagttcgctcgtttgatgtctttaacacttgcatatagatcacattatggataggcttggcttgtaacattgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA
       |||  ||   |||   || |     | || |||  || | | |  | | |||  |||  |   || || | ||  ||||| | || |  |    | ||| | || ||||||||||||||  | || || || || ||| ||||||| ||||||||||||||||| ||||| ||||||||||| ||| |  | ||    |
ttgctccacatacttt-gtttattcatccaccg-ctgtaat-ctggtaaaagggtaacacgatgcctct-ctcggttggt--cattgggttgttggttggctacagATCGGTCGTTACCCGAGGCACGTGATCAGCCTGTTCTTCCGGCTGCTGTATCCGTGGTACTGGCCTTCCTCTTGCTGGAACTTCGTGATGACCTGTGCCA

upper sequence: AT5G59960.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G07000.1 (Glycine max), 3'ss of exon 10
aacaggctcaagttcgctcgtttgatgtctttaacacttgcatatagatcacattat-ggataggcttggcttgtaacattgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA
|  || |   |||||    |  |||  |   |  ||    ||   |  |  || |||   |||      | | || |  || |  |  |    |  | ||||| || ||||||||| ||||||| |||||| | || |||||| |||| ||||||||||| ||||| ||||| || |||||||| ||||||||||||||| 
ataagaccttagttcttgggagtgagctacatg-catacacaagcatgttccactattatataaataatgatagtgatgttattgttatacaatgatacagGTGGGACGTTACCCGCGGCATCTTATTAGTTTGTTCTTCAGGTTGCTTTATCCGTGGTATTGGCCTTCCTCTTGTTGGAACTTCGTGGTTTCTTGCATTC

upper sequence: AT5G59960.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G15030.1 (Glycine max), 3'ss of exon 10
aacaggctcaagttcgc-tcgtttgatgtctttaacacttgcatatagatcacattatg--gataggcttggcttgtaacattgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA
       |  | ||||  || ||    |      |||     | | |    |  ||       |     |   |  | |  || |  |  |    |  | ||||| || ||||| ||  ||||||| |||||| | || |||||| |||| ||||||||||| ||||| ||||| || |||||||||||| ||||||||||| 
---gtcttttatttcgagtcattcagagcgagctacatgcatacacaagcaatgttcctctattttatataagtgatgatgttattgttataccatgatacagGTGGGACGTTATCCTCGGCATCTTATTAGTTTGTTCTTCAGGTTGCTTTATCCGTGGTATTGGCCTTCCTCTTGTTGGAACTTTGTGATTTCTTGCATTC

upper sequence: AT5G59960.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g04350.t01 (Vitis vinifera), 3'ss of exon 10
--aacaggctcaagttcgctcgtttgatgtctttaacacttgcatatagatcacattatggataggcttggcttgtaac-attgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA
    || |||     |  || |  || |   | ||||        ||   |    | |||  || |   |  ||||    | | |||| |   ||   |||||||||| || || ||  | ||||||||||| ||||| ||| |  |||||||||| ||||||||||| || || || ||||||||  |  | |||||||| |
ctttcatgcttttaatatctggactgttaaatctaacctcattccatcttttttctaatgtttacgggggatttgtggtgactttgatac---tggaatgcagGTTGGACGGTATCCTCGACATCTCATTAGCCTATTCTTCCGATTGCTATATCCATGGTACTGGCCTTCGTCTTGTTGGAACTTCATAATGTCTTGCATAA

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|86084500|gb|DR380259.1|DR380259
EST:     CAAGAGCCGTCCGTCATGCAGCCTGGGATGCTTTGGATTCCCTCTTTCCT                         GTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATAT
genomic: CAAGAGCCGTCCGTCATGCAGCCTGGGATGCTTTGGATTCCCTCTTTCCTgtgagtatta ... tgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATAT
EST: gi|125306685|gb|EL320770.1|EL320770
EST:     CAAGAGCCGTCCGTCATGCAGCCTGGGATGCTTTGGATTCCCTCTTTCCT                         GTTGGGCGTTACCCGAGGCATCTCA
genomic: CAAGAGCCGTCCGTCATGCAGCCTGGGATGCTTTGGATTCCCTCTTTCCTgtgagtatta ... tgtcttgcagGTTGGGCGTTACCCGAGGCATCTCA
EST: gi|125185626|gb|EL200580.1|EL200580
EST:     CAGCCTGGGATGCCTTGGATTCCCTCTTTCCT                         GTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATAT
genomic: CAGCCTGGGATGCTTTGGATTCCCTCTTTCCTgtgagtatta ... tgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATAT
EST: gi|124732203|gb|EH823605.1|EH823605
EST:     ATGCTTTGGATTCCCTCTTTCCT                         GTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATAT
genomic: ATGCTTTGGATTCCCTCTTTCCTgtgagtatta ... tgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatcacattatggataggcttggcttgtaacattgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA
                         ttgtaac  putative branch site (score: 2)
                                         ctcttgtctt  putative PPT
     acattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaggctcaagttcgctcgtttgatgtctttaacacttgcatatagatcacattatggataggcttggcttgtaacattgtgatgctcttgtcttgcagGTTGGGCGTTACCCGAGGCATCTCATTAGTCTATTTTTCAGGCTGCTATATCCGTGGTACTGGCCATCCTCATGCTGGAACTTTGTGGTTTCTTGCATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - ttaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctct