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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggtttaatgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G79530.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
gtatgct-tcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggtttaatgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG
   |||  || |  | || ||  | | ||  ||||   || || |   |  |||     | |||  | || |||  |   |  | |  |    |||     ||    |||   || ||||| ||  | || ||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||| ||||
-actgcggtcatgcacttgtaccgtctga--agattctgtgat-gtgcctgtatgtaacattgtgaatcttttatcagatttac-tcataagctgtgtgtttc----agGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 11
gtatgcttcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgt-ttaatgtagaactcttaata-acctctcatggtttaatgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG
   ||  | || |     |||| |        ||   |  |  ||| |||   | | |||  |   |||    | |  | ||  ||   | |  |       | |  ||||   || ||||| ||  | || ||||| ||||| || |||||||| || ||||| || ||||||||||| || |||||||||||
--gtgtgttctgatgcactattcctaagatttatgcagaga--gaaccatgtgcatattatcgaccaacctacagtggatcttacacaatctttt------ttttttcagGACGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGATGTTGTTTCCAATGATTTTGTTGGTGATTCAAG

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
gtatgcttcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggttta---atgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG
|||||  |  |    |||| ||    |        ||  ||        | || |||   |    | || ||  |    |   |||  ||    |   |||  | | | ||| |||||||||| ||||| || ||||| || || ||||||||||| || ||||| ||||| ||||| || || |||||||||||
gtatgtctattgcgttttttttttttgg-------tctccactctgctgtgattgttctgtactaaccttttgcttgatttctatgactttgctactgaaaaatatga-agGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 11
gtatgcttcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggtttaatgt--aaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG
|||||  |  |    |||  ||    |  |    | | |||| |     | || |||   ||||    | |   | |  |||     |||  |    |||  | | | ||| |||||||||| ||||| || ||||| || || ||||||||||| || ||||| ||||| ||||| || || |||||||||||
gtatgtctattgctttttgtttttttgctc---caccctcattgc--tgtgattgttc--tgtaaccttttgcttgatttctatgactttgctactgaaaaatatga-agGTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG

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|86075867|gb|DR371624.1|DR371624
EST:     TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAA                         GCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGMAGA
genomic: TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAAgtatgcttcc ... cctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGA
EST: gi|86077225|gb|DR372982.1|DR372982
EST:     TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAA                         GCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGA
genomic: TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAAgtatgcttcc ... cctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGA
EST: gi|86082375|gb|DR378134.1|DR378134
EST:     TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAA                         GCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGA
genomic: TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAAgtatgcttcc ... cctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGA
EST: gi|125245527|gb|EL259612.1|EL259612
EST:     TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAA                         GCATGCCTCAGAAGG
genomic: TGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAAgtatgcttcc ... cctctaacagGCATGCCTCAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttaatgtagaactcttaataacctctcatggtttaatgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG
                                             cctct  CT-rich tract
                                  tttaatgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggtttaatgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG