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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaattatttgacctgatggaaatagatattttccagttaaatttctcttgttttgaccctgatctgatgctggaggtctatcatgtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 5
gttagaattatttgacctgatggaaatagatattttccagttaaa-----tttctcttgttttgaccctgatctgatgctggaggtcta---tcatgtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG
|||||    ||      |||    |  |  |  |||    ||  |     ||  | |  ||||     | ||||  || |     | |    |||| | |  ||||||  ||||||| ||||||||||||||||| |||||||| |||   |||||||| || || |||
gttagtggcatgctttatgaatccataattttctttttgcttggaaaccattcatatatttttttagttcatctagtgatcataatttgccttcattttcatatagATTTCTAAAGGGCTTTTGGAGAAATATGGCCCTGAGAGGGTTCTGGATACCCCAATCACAGAG
















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|164016936|gb|ES123772.1|ES123772
EST:     GTTGGCCAATATCAAGGTGCCTACAAG                         ATCACTAAAGGCCTTTTGGAGAAATATG
genomic: GTTGGCCAATATCAAGGTGCCTACAAGgttagaatta ... gtactcatagATCACTAAAGGCCTTTTGGAGAAATATG
EST: gi|164137578|gb|EL978552.1|EL978552
EST:     GTTGGCCAATATCAAGGTGCCTACAAG                         ATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
genomic: GTTGGCCAATATCAAGGTGCCTACAAGgttagaatta ... gtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
EST: gi|116443796|gb|EG486388.1|EG486388
EST:     GTTGGCCAATATCAAGGTGCCTACAAG                         ATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
genomic: GTTGGCCAATATCAAGGTGCCTACAAGgttagaatta ... gtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
EST: gi|125153757|gb|EL184737.1|EL184737
EST:     GGTGAAGAGGTTGGCCAATATCAAGGTGCCTACAAG                         ATCACTAAAGGCCTTTTGGAGAAATATGGT
genomic: GGTGAAGAGGTTGGCCAATATCAAGGTGCCTACAAGgttagaatta ... gtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGT
EST: gi|125294944|gb|EL309029.1|EL309029
EST:     TGGCCAATATCAAGGTGCCTACAAG                         ATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
genomic: TGGCCAATATCAAGGTGCCTACAAGgttagaatta ... gtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
EST: gi|116376958|gb|EG419550.1|EG419550
EST:     GTTGGCCAATATCAAGGTGCCTACAAG                         ATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
genomic: GTTGGCCAATATCAAGGTGCCTACAAGgttagaatta ... gtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACC
EST: gi|125265385|gb|EL279470.1|EL279470
EST:     GTTGGCCAATATCAAGGTGCCTACAAG                         ATCACTAAAGGCCTTTTGGAGAAATATGGT
genomic: GTTGGCCAATATCAAGGTGCCTACAAGgttagaatta ... gtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttctcttgttttgaccctgatctgatgctggaggtctatcatgtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG
        ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaattatttgacctgatggaaatagatattttccagttaaatttctcttgttttgaccctgatctgatgctggaggtctatcatgtactcatagATCACTAAAGGCCTTTTGGAGAAATATGGTCCTGAGAGAGTTTACGATACCCCTATTACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA