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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataacaatggaaagaatcagatttaatctaattgaaacattttctgagtctttcatggtttatgcatgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG

Basic information

species Arabidopsis thaliana
transcript AT4G22130.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g42800.1 (Oryza sativa), 3'ss of exon 13
--------------------gtaataacaatggaaagaatc---agatttaatctaattgaaacattttctgagtctttca--tggtttatgcatgtcaa--cagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
                        || ||||| |   | |    | |||| ||||  ||    | |    |   |||||    |     |||  |    |  |||||||||||| ||||| | || || |||||||| ||||| |||||||||||  |||| ||||| || || || |||||||| || |||| |||||||||||
gtaagtaatgtagtaccacatctctatcaatgtagttatttccaacatttcatct--ttaggtcctacagtagttctttgggctaaaccatgtgttatgatgcagGTTTCAACTGAAGTGTTTGGATCTTTTGGATATAGCGCCCCAGAGTTTGCCATGTCAGGAATATATACTGTAAAAAGTGACGTGTACAGTTTTGGAGTAG

upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 13
-----------------------------------gtaataacaatggaaagaatcagatttaatctaattgaaacattttctgagtc--tttcatggtttatgcatgtcaa--cagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
                                   |  | |    |   | |     | ||   ||   | |||  | ||  | | |    |  ||    |  |  || ||   |||||||||||| | ||| | || |||||||||||||| || || ||||||||  |||| |||||||| || || || |||||||| |||| ||||||||| |
gtcagtcataccaccacatttctaaacttctggttgctaaagttctcagatggccttgtttggctcctgtagaagtagttaattaatggactgaatatgcttggtttgccattccagGTTTCAACTGAGGTGTTTGGCTCATTTGGATACAGTGCCCCGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTG

upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 13
----------------------------gtaataacaatggaaagaatcagatttaatctaattgaaacattttctgagtctttcatggtttatgcatgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
                            ||        |  ||| |  ||  | |    || ||   || | |||   || ||   |  ||      |  |  |||||||||||| ||||  | || |||||||| || ||||| |||||||||||| |||| || ||||| || || || || |||||||||| ||||||||| |
gcaagtaacacacatctcttccactgaggtttcttttcttcaaatacccatttctgga-tagtttctacttattccatgtattaactaattggcctgtcactgcagGTTTCAACTGAAGTATTTGGATCATTTGGCTATAGCGCCCCAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGG

upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G00970.1 (Glycine max), 3'ss of exon 13
------------------gtaataacaatggaaagaatcagatttaatctaattgaaacattttctgagtctttcat---ggtttatgcatgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
                  ||       ||| | ||    | |||   | |   |     ||||      ||||| ||     |   ||  | | ||||||| ||||||||  |||| ||||||||||| || || ||||| ||||||||| | || ||| | ||||| || ||||||||||| ||||  ||||| || |
gttggagaagaagcttttgtttccttcatgcacagctgaacattgtttttgtatcttttatttctcacttctttgattaccatcattgagttttaacagGTATCAACTCAGATGGTCGGTTCATTTGGTTATAGTGCTCCTGAGTTTGCATTATCTGGAGTATACACTGTAAAAAGTGATGTTTACAGCTTTGGGGTGG

upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G11820.1 (Glycine max), 3'ss of exon 13
------------------gtaataacaatggaaag--aatcagatttaatctaattgaaacatttt-ctgagtctttcatggtttatgcatgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
                  ||       ||| | ||   | ||   ||  | ||  |   |  | |  ||   |   | |   |    |  | ||||||||| ||||||||  |||| |||||||| || || || ||||| ||||||||| | || ||| | ||||| || ||||||||||| ||||  ||||| || |
gttggtaaagatgcctttgtttccttcatgcatagctgaacatggtttttgtatctattatttctcactacattgattacaatcatcgagtttcaacagGTATCAACTCAGATGGTCGGTTCATTCGGTTATAGTGCTCCTGAGTTTGCATTATCAGGAGTATACACTGTAAAAAGTGATGTTTACAGCTTTGGGGTGG

upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 13
---------------gtaataacaatggaaagaatcagatttaatctaattgaaacattttctgagtctttcatggtt-tatgcatgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
                 |||  |  |   ||| ||   |     |||  ||   |  | | ||   |      || || ||||    |  |||||||||||||||  |||| ||||||||||| ||||| ||||| || |||||  | || || || ||||| || ||||| ||||| ||||  ||||| || |
gtaaataaatggggttgaattcctgtcttaagtattttacagtttctcttttgtatgtctgcttgatacaaattgtttctatgatgtttgacagGTTTCAACTCAGATGGTTGGTTCATTTGGTTACAGTGCTCCTGAATTTGCTTTATCTGGTATATACACTGTAAAAAGCGATGTGTACAGCTTTGGGGTGG

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|125253315|gb|EL267400.1|EL267400
EST:     TTGACACCTAACACTGAGAGACAG                         GTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTCTTGC
genomic: TTGACACCTAACACTGAGAGACAGgtaataacaa ... atgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGT-TTGC
EST: gi|164028562|gb|ES013919.1|ES013919
EST:     GACAGTGGTTTAGCTGCTTTGACACCTAACACTGAGAGACAG                         GTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCA
genomic: GACAGTGGTTTAGCTGCTTTGACACCTAACACTGAGAGACAGgtaataacaa ... atgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaatctaattgaaacattttctgagtctttcatggtttatgcatgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
     atctaat  putative branch site (score: 3)
        taattgaaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataacaatggaaagaatcagatttaatctaattgaaacattttctgagtctttcatggtttatgcatgtcaacagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG