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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttaagctgtgtataaatatcattggattgtgttatgctcacctaaccttacattcatttctgtcctctatgaagttgttgtttggactcattattctgctgttaatcatgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT

Basic information

species Arabidopsis thaliana
transcript AT5G26830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 5
gtgggttaagctgtgtataaatatcattggattgtgttatgctcacctaaccttacattcatttctgtcctctatgaagttgttgtttggactcattattctgctg--ttaatcatgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
                ||||  || |  | |||   | | || |     | || |  |    || | ||   | |||  || |   ||  | |  |||||    ||  ||     | ||||||||| |||| ||||  ||||||| ||||| ||||||||| || ||||||||||| ||| | || ||  | || ||||| || ||||| || |||||||
----------------ataagcataagcgaatta-atgaggccctaaatatct-atttctgcttatatcacatttgagatttta--ttaaattttttatttgtttgaattgtgtttctagGTTGAAATCATTAATGAGTTGCCTGAAGACAAGACCATTACAGTATACAGATGTGGTCCTCTAGTTGACCTTTGCCGTGGGCCACACATCCCCAATACTT

upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 5
gtgggttaagctgtgtataaatatcattggattgtgttatgctcacctaaccttac-attcatttctgtcctctatgaagttgttgtttggactcattattctgctg-ttaatcatgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
    |  |   |   |   | | || |  | |||| | || |     | |  || |   | || |      | |||     |    |     || |  |    |    |||    |  |||||||| |||| ||||  |||||||  |||| |||||||||||| ||||| ||||| ||||| || ||  | || ||||| || ||||| ||||||||||
----gcaaccttccttgctactgtctt--gtttgtttcattcctctatcattttgctgcttatgttaaatatatatacgacttccatccattcttacaaaaaagtgaattatatgttcagGTTGAAATCATTAATGAGTTGCCTGAGGACAAGACCATTACTGTATACAGGTGTGGTCCTTTAGTTGACCTATGCCGTGGGCCACACATCCCAAATACTT

upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 4
gtgggttaagctgtgtataaatatcattggattgtgttatgctcaccta-accttacattcatttctgtcctctatgaagttgttgtttggactcattattctgctgttaat-catgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
               | | |     |||    | | || |  ||||||| |  ||| | |  ||| | ||    || ||       |||||     |   ||||  |||| |      |||||||  | ||||||| ||||||||| ||||  || ||||| || |||||||||||||| ||||| ||||||||||||||||| || ||||| ||||| |
--------------atctgagccatatttc-ctattttct-ttcacctataatttataattttttatatctcaaattaa----caatttggtgctttggctctgtggttattgtgatcagGTTGAGATTATCAATGATTTGCCTGCCGACAAAACTATTACAGTATACAGATGTGGCCCCTTGGTTGATTTGTGTCGTGGACCCCATATACCTAATACAT

upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------gtgggttaagctgtgtataaatatcat-tggattgtgttatgctcacctaaccttacattcatttctgtcctctatgaagttgttgtttggactcattattctgctgttaatcatg--tagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
                                                                              ||   || |  |   |     ||| || ||     |||| | ||    |   |   || |  ||| | |     |  || |     ||| |     |   ||    |||| |||||   || | ||  | ||||||| ||||||||| ||||  || || || || ||||||||||| || |||||||||||||||||||| || || ||||| ||||| |
gcaagtataacttttttttcttctttgagggtgaggtggggtgtggataagcttcttgttttcatgatcttatctattgttttttgaattacatcatcttattatctgagccatgtt-tcctattttcttccaccaattttttttatatctcacaaattaacaatttagtgctttggctccatggtta-tcatgatcagATCGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGATGTGGTCCCTTGGTGGATTTGTGTCGTGGGCCCCATATACCTAATACAT

upper sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 5
gtgggttaagctgtgtataaatatcattggattgtgttatgctcacctaaccttacattcatttctgtcctcta-tgaagttgttgtttggactcattattctgctgttaatcatg--tagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
||| || |||||   | |  |||||||         ||  |||  ||| | || || | | | | |     ||| |    |||||  |   |    || || |    |   ||||    || ||||| |||||||||  || || | |||||  || || || || ||||||||||| || ||||| ||| |||| |||||||| || ||||||||||| |
gtgagtgaagctccatttttatatcatccataccatttgagctatccttagct-acttccttattttcttactactcttattgttactcatatgggttgtt-tatcatatctcataatcagATTGAAATCATCAATGACTTACCCGAAGACAAAACTATCACAGTATACAGATGTGGGCCATTGGTTGATCTGTGCCGTGGACCCCATATACCAAATACAT

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|164102653|gb|ES042976.1|ES042976
EST:     AAGTGACGAAGGATCAGGCACTCGAGATGTTTTCTGAGAATAATTTTAAG                         GTTGAACTCATCAATGGT
genomic: AAGTGACGAAGGATCAGGCACTCGAGATGTTTTCTGAGAATAATTTTAAGgtgggttaag ... aatcatgtagGTTGAACTCATCAATGGT
EST: gi|164217302|gb|EL968369.1|EL968369
EST:     GTTTTCTGAGAATAATTTTAAG                         GTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACA
genomic: GTTTTCTGAGAATAATTTTAAGgtgggttaag ... aatcatgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtcctctatgaagttgttgtttggactcattattctgctgttaatcatgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
                                         tgttaat  putative branch site (score: 3)
                             tcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttaagctgtgtataaatatcattggattgtgttatgctcacctaaccttacattcatttctgtcctctatgaagttgttgtttggactcattattctgctgttaatcatgtagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA