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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtcttagcttctatgttcaactcaagatcatgttcttgtcattgaagttttaaacagagattgatgttttcaaatttcaatgcttagaaaatctattcttagagtctatgtatagagatacatagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG

Basic information

species Arabidopsis thaliana
transcript AT2G14285.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G14285.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
gtatggtcttagcttctatgttcaactcaagatcatgttcttgtcattgaagttttaaacagagattgatgttttcaaatttcaatgcttagaaaatctattcttagagtctatgt-atagagatacatagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG
                                                                         | | ||||| |  | ||||    | || | |||||||     | |    | ||| || ||    ||   | |    ||||||     ||  ||  ||||  | || |||| |  || || ||||| |||||||||||||||||  | |||||||| ||||||||| |||||||
------------------------------------------------------------------------gtactaatttgacagtttagctgttgtactgttagagtgatcatcactagggtac-taaatgacatacaaaat----tcattgctgcctt--atttttgtactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG

upper sequence: AT2G14285.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G058252_T01 (Zea mays), 3'ss of exon 3
gtatggtcttagcttctatgttcaactcaagatcatgttcttgtcattgaagttttaaacagagattgatgttttcaaatttcaatgcttagaaaatctattcttagagtctatgtatagagatacatagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG
                            |  |   ||    | |   ||   |  || |  |    || ||| || ||      |      ||| | ||| || |  | |   |    |  || | | | |      ||||||||  | |       | ||   |   |  |   || |||| |  ||||| ||||| ||||||||||| |||||  | |||||||| ||||||||| |||||||
--------------------------gtactaatttggcagtttggctgtcatactataagggtggtggtgtattgaatgcgtgagat---gaatagctaatcatctattgggtactgaatgacatacaaa------attcattgctgcc-------tcttttttttctactgcgtgcagCTTGCCAACACTGAGGAGTACATTGATGGTCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG

upper sequence: AT2G14285.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
gtatggtcttagcttctatgttcaactcaagatcatgttcttgtcattgaagttttaaacagagattgatgttttcaaatttcaatgcttagaaaatctattcttagagtctatgtatagagatacatagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG
                                                                     |||||         ||      |  || || || | || || | |||||| |   |    | | | | ||   |  || |   || || | |         |||| || |||| |  ||||  || |||||||||||||| || || || ||||||||||||||||||||||||||
-------------------------------------------------------------------tttgtttctgctaccaaactggctgctaagct-ttgtcagtgtttgtgtatatactgat---ggttggtgatgtttcataattcatgggaatct---------ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG

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|116465383|gb|EG507975.1|EG507975
EST:     GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
genomic: GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
EST: gi|116436072|gb|EG478664.1|EG478664
EST:     ACTCCTACATGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGAAGGGCAATTGACAGGAAACCTTGGA
genomic: ACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
EST: gi|116436039|gb|EG478631.1|EG478631
EST:     GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGATGG
genomic: GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGG
EST: gi|116465427|gb|EG508019.1|EG508019
EST:     GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
genomic: GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
EST: gi|116465372|gb|EG507964.1|EG507964
EST:     GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
genomic: GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
EST: gi|116465361|gb|EG507953.1|EG507953
EST:     GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
genomic: GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
EST: gi|116435994|gb|EG478586.1|EG478586
EST:     GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGTAG                         CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
genomic: GTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
EST: gi|125195321|gb|EL210275.1|EL210275
EST:     TGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
genomic: TGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGA
EST: gi|125225113|gb|EL239198.1|EL239198
EST:     GGTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAG                         CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTT
genomic: GGTTTTCTCGCTTCTGTTGACTCCTACATGAACTTGCAGgtatggtctt ... ttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG
                                         cttgtttttt  CT-rich tract
         tttattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtcttagcttctatgttcaactcaagatcatgttcttgtcattgaagttttaaacagagattgatgttttcaaatttcaatgcttagaaaatctattcttagagtctatgtatagagatacatagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA