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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgcaaaagagtatatagatcctttcatttttaccccaacttatcatactgaatcaaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG

Basic information

species Arabidopsis thaliana
transcript AT5G19220.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------gtgaatgcaaaagagtatatagatcctttcatttttaccccaacttatcatact-gaatc----aaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG
                                                      || | ||    || ||| ||    |  ||||       |      ||| | | ||     ||| |   |  | ||||  | |   ||  |   | | ||  || || || || |||||||| || ||||||||||| |||| ||||||||||||| |||| ||||||||||| |||||||| ||  | || ||||||
gtgattcctgtaccatttcagtagcttcatccatgaacaatgaagtgacctctcataccaagttttagataaattgaattgttttatttggtaagagaaatatttggattttgaaaatacactactctctttcatttgtttatttcgtccttgtcagCCGGGCATCTGATTTTGGTCTAATGAAGATAGACGACACAGGAAGAGTTATCGCATTTAGTGAAAAACCAAAAGGAGATGATTTAAAGGCAATG

upper sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 2
---gtgaatgcaaaagagtatatagatcctttcatttt--taccccaacttatcatactgaatcaaagatcatgatttcttat-agtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG
   | | || |   | | | | |   | | |  ||||   ||||||   |  || |  |        |    ||||     || ||| ||||| |      |||  || || || || |||||||| || ||||||||||| ||||  ||||| || || ||||||||||| ||||| |||||||||||  | || ||||||
tttgagcatccgctaaactctct---ttcatgtatttccataccccgtttggtcctggtctccttgtggatttgatcatgaatgagtttcttttt-----tatgtcagCCGGGCATCTGATTTTGGCCTAATGAAGATAGACGACACTGGAAGGGTAATTTCATTCAGTGAGAAACCAAAAGGAGACGAATTAAAGGCAATG

upper sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 6
--gtgaatgcaaaagagtatatagatcctttcatttttaccccaacttatcatactgaatcaaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG
   |   | | | | ||   |    |   ||    |||     ||  | | ||  |   ||| | || |    || ||| |      || |     |||| ||| |||||||| |||||||| || |||||||||||  | |||||||| ||  | || || ||||||||||| |||||||| || ||||||||||||
gctttgttacgataaagcccacgactgaattagagttt-taataatatttaattatttgtcatatattac---tttttaaaactctattgtgcaatcatgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG

upper sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 6
gtgaatgcaaaagagtatatagatcctttcatttt--taccccaacttatcatactgaatcaaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG
 | ||   |||| | ||  | ||  |    ||||   || |  | ||||  |   |  |||| | || |    |  ||| |      || |     |||| ||| ||||||||||||||||| || |||| ||||||  |||| |||||  |  | ||||| |||||||| || |||||||| ||  |||||||||||
atcaacctaaaacaatagct-gactcaacaatttggatatctaagcttaaaaacgtttatcatatattac---tgattaaaactctattgtgcaaccatgatagCCGTGCCTCAGATTTTGGTCTGATGAGGATAGACAACAAGGGAAGGATCCTTTCATTTAGTGAAAAGCCCAAAGGAGAAGAGTTGAAAGCAATG

upper sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------gtgaatgcaaaagagtatatagatcctttcatttttaccccaacttatcat-actgaatcaaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG
                                    ||     |    | |   |    |  ||  ||  |  |||   ||  | | |    ||  || |  |     | ||    ||| | ||| ||| |||| ||| ||||| |||||||| ||  | |||||||||||  |||||||||| ||| |||  ||||||||||| ||||||||||| ||  |||| ||||||
gtaggttctatttcctatactggtttcaactctttatgctattagccaaatgcctgagcctctttgttcatgtccctgttttcctttagatgattgaaaactac--ccttttgagttctttctctctttccatgatagCCGTGCTTCAGATTTCGGTTTAATGAAGATAGACAACAAAGGAAGGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG

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|125102942|gb|EL157521.1|EL157521
EST:     TATAAGCATTTCCTGCATACCAATAGATGACAG                         ACGTGCCTCAGATTTTGGGCTTA
genomic: TATAAGCATTTCCTGCATACCAATAGATGACAGgtgaatgcaa ... tacatggtagACGTGCCTCAGATTTTGGGCTTA
EST: gi|125232740|gb|EL246825.1|EL246825
EST:     GCGGATATAAGCATTTCCTGCATACCAATAGATGACAG                         ACGTGCCTCAGATTTTGGGCTTA
genomic: GCGGATATAAGCATTTCCTGCATACCAATAGATGACAGgtgaatgcaa ... tacatggtagACGTGCCTCAGATTTTGGGCTTA
EST: gi|124948130|gb|EL023917.1|EL023917
EST:     CGGATATAAGCATTTCCTGCATACCAATAGATGACAG                         ACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTAT
genomic: CGGATATAAGCATTTCCTGCATACCAATAGATGACAGgtgaatgcaa ... tacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTAT
EST: gi|125123435|gb|EL169884.1|EL169884
EST:     ATATAAGCATTTCCTGCATACCAATAGATGACAG                         ACGTGCCTCAGATTTTGGGCTTA
genomic: ATATAAGCATTTCCTGCATACCAATAGATGACAGgtgaatgcaa ... tacatggtagACGTGCCTCAGATTTTGGGCTTA
EST: gi|125193929|gb|EL208883.1|EL208883
EST:     CGGCAGAGTGGCGCGGATATAAGCATTTCCTGCATACCAATAGATGACAG                         ACGTGCCTCAAGATTTTGGGCTTATGAAGATAGATGAC
genomic: CGGCAGAGTGGCGCGGATATAAGCATTTCCTGCATACCAATAGATGACAGgtgaatgcaa ... tacatggtagACGTGCCTCA-GATTTTGGGCTTATGAAGATAGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatactgaatcaaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG
                                 tctctttctatttac  CT-rich tract
                      atttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatgcaaaagagtatatagatcctttcatttttaccccaacttatcatactgaatcaaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA