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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattactggcctcttctctctttccgatccctgaagtcaaagacagactagtattggaacaactgttaaaaaaatattatttttccctgcttttttcattctcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAACATATAGTAGATCATATGGACTTGTGGCTCTCTGAGTGTCGTGGAGGGAT

Basic information

species Arabidopsis thaliana
transcript AT4G36195.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36195.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 12
gtatattactggcctcttctctctttccgatccctgaagtcaaagacagactagtattggaacaactgttaaaaaaatattatttttccctgcttttttcattctcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAACATATAGTAGATCATATGGACTTGTGGCTCTCTGAGTGTCGTGGAGGGAT
 || | || |    |  |  |      | |||    || | |      ||  | |  | |  |      ||||  || ||| |   |  ||| || |    ||    | ||||||| ||   ||||| |||   ||||||||||||||  ||||||| |||||||| ||   ||| ||||||||||||||||| |||||||| |  | ||| | 
-taaaataataatattatagcaagcagcaatc----aaattatgt---gatcaatgattgtgctg--agtaaactaacattctgaatttctggttgtgaattt----tgttcagGTAATGAGAAGAACTGCTCCTCACCTGATGCAGTTCACAAAGTAAGGCAACAGATTACAGAACATATGGACTTGTGGCTATCTGAGTGCCAAGAAGGCAG

upper sequence: AT4G36195.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 11
gtatattactggcctcttctctctttccgatccctgaagtcaaagacagac-tagtattggaacaa----ctgttaaaaaaatattatttttccctgcttttttcattctcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAACATATAGTAGATCATATGGACTTGTGGCTCTCTGAGTGTCGTGGAGGGAT
                 | |  | ||| ||    | | | |||||| || | |   ||||   |      |  ||  |  |||  |     |  |  ||| || | || |  | |||||||||| ||||||| || || || |||||||||||  ||||||| |||||||| ||  |||| || || ||| ||||||| ||  |||| |  |       
-----------------tgtggcattctgacaaattatg-caaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggt-ttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG
















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|164011221|gb|ES007262.1|ES007262
EST:     CCATGGAAGTGATCTCCGTGGATGCCCTCAATCTCCCATGGTCATTGGAG                         GTGATTCCAAGAATT
genomic: CCATGGAAGTGATCTCCGTGGATGCCCTCAATCTCCCATGGTCATTGGAGgtatattact ... tcatattcagGTGATTCCAAGAATT
EST: gi|164230530|gb|ES162941.1|ES162941
EST:     CCATGGAAGTGATCTCCGTGGATGCCCTCAATCTCCCATGGTCATTGGAG                         GTGATTCCAAGAATT
genomic: CCATGGAAGTGATCTCCGTGGATGCCCTCAATCTCCCATGGTCATTGGAGgtatattact ... tcatattcagGTGATTCCAAGAATT
EST: gi|86079905|gb|DR375662.1|DR375662
EST:     CCATGGAAGTGATCTCCGTGGATGCCCTCAATCTCCCATGGTCATTGGAG                         GTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAAC
genomic: CCATGGAAGTGATCTCCGTGGATGCCCTCAATCTCCCATGGTCATTGGAGgtatattact ... tcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAAC
EST: gi|164203326|gb|ES026695.1|ES026695
EST:     CAATCTCCCATGGTCATTGGAG                         GTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAAC
genomic: CAATCTCCCATGGTCATTGGAGgtatattact ... tcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacaactgttaaaaaaatattatttttccctgcttttttcattctcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAACATATAGTAGATCATATGGACTTGTGGCTCTCTGAGTGTCGTGGAGGGAT
                       tttttccctgcttttt  CT-rich tract
     actgttaaaaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattactggcctcttctctctttccgatccctgaagtcaaagacagactagtattggaacaactgttaaaaaaatattatttttccctgcttttttcattctcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAACATATAGTAGATCATATGGACTTGTGGCTCTCTGAGTGTCGTGGAGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG