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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatctctcatacctttaatcactttaggccttctagttttttgttatatgaacctgatctgtgtttaaagtctctataagccggctaatttggttcacaaaccttttcttttag

Basic information

species Arabidopsis thaliana
transcript AT5G03406.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03406.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G158228_T01 (Zea mays), 5'ss of exon 3
TGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatctctcatacctttaatcactttaggccttctagttttttgttatatgaacctgatctgtgtttaaagtctctataagccggctaatttggttcacaaaccttttcttttag
| || | || || || ||| |||||||| | |||||  |||||||  | || || |||||||| ||||||||||||||  ||||||||||| |||||   |||   | |  ||  |  | |     ||  | ||    | | || |     | ||||| |||| ||   ||    |||   |   |    ||                           
TACTATAGGACAATGCTGGCGATATGAGCGCATGACCAGAGGAAGAAGGCGGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtac-cacccttctcatttattgattctggatgctgctttgcttgtatacctttgaac-tgatttggcattgccatcttgttgttcgaattag--------------------------

upper sequence: AT5G03406.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G34050.1 (Glycine max), 5'ss of exon 4
TGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatctctcatacctttaatcactttaggccttctagttttttgttatatgaacctgatctgtgtttaaagtctctataagccggctaatttggttcacaaaccttttcttttag
  ||||||| || |||||| | || |||||||||||| | ||  | || |||||||| ||||| ||||| ||||||||||||||||| || |  ||||  ||||||    | |       | ||      |    ||  |||| |   || |     |||  |    || | | || || || |   |    || || | || ||| ||          
CACTGTTGGACAATGTTGGCGGTACGAGAGAATGACAAGGGGGCGTCGTCGTGAGCACTACCAATGGAACATGGATATTATTGGTGTTCCCGGGGTTATGgtatgtgctgcactgctgcctgatatacacactttttgaagttatggattgt-----cctctttctggtctgatgtttc-atga-ttgat--atctgatccaaaaagct----------

upper sequence: AT5G03406.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv08s0040g01360.t01 (Vitis vinifera), 5'ss of exon 4
TGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatctctcatacctttaatcactttaggccttctagttttttgttatatgaacctgatctgtgtttaaagtctctataagccggctaatttggttcacaaaccttttcttttag
|||||| || ||||||||| | ||||||||||||||| | ||| | || |||||||| ||||| |||||||||||||| ||||||||||| || ||||  || |||     || || | | | ||  |  |    ||||     | | ||  ||    |  | |  |  ||| | | |  |    |   | ||    ||| |   |             
TGCTGTAGGACAGTGTTGGCGTTATGAGAGAATGACAAGGGGACGCCGTCGTGAGCACTACCAATGGAATATGGATATCATTGGTGTGCCAGAGGTTATGgtgtgt---cttcctaacctaagtctatggaaagattct----ctctcttccatcgctccaaacaatcattacactattaaattacttaccaaccctgtttaattat------------

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|116436932|gb|EG479524.1|EG479524
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436934|gb|EG479526.1|EG479526
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436926|gb|EG479518.1|EG479518
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436944|gb|EG479536.1|EG479536
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436933|gb|EG479525.1|EG479525
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436929|gb|EG479521.1|EG479521
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436941|gb|EG479533.1|EG479533
EST:     GTGAGCATTACCGGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436930|gb|EG479522.1|EG479522
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436940|gb|EG479532.1|EG479532
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436943|gb|EG479535.1|EG479535
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436931|gb|EG479523.1|EG479523
EST:     TGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: TGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
EST: gi|116436945|gb|EG479537.1|EG479537
EST:     GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACA                         GCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA
genomic: GTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatct ... tttcttttagGCTGAAGCAGAACTAATTTCATCTATAATGACATTCTTCAAGCGAATTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatctctcatacctttaatcactttaggccttctagttttttgttatatgaacctgatctgtgtttaaagtctctataagccggctaatttggttcacaaaccttttcttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG