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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacacgtagaatatactgtgtacataaaattgtatctcattacttgtttcacaagagagctatcatgtgctaatgtacttacttttgcatattcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 15
gtgaacacgtagaatat---actgtgtacataaaattgtatctcattacttgtttcacaagagagcta-tcatgtgctaatgtact-tacttttgcatattcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG
||   |   ||    ||   | ||  ||      ||   ||  | || ||| |||  || || |   | |  |||  |    |||  | |   |   |   ||||||||  |||| ||||| || || |||||||| ||||||||| | |||||||| || || |||||||||||||| ||||| |||
gtatccttttaattcatttcaatgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacagAGAAACATGATACGTGAGGCAACAGCTTTCCTGCTGGATGTTTTAAAGCCAAACTTGCCGGAGCATGCTTTTCTTCAAACCAAG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 13
------------------------------------gtgaacacgtagaatatactgtgt-acataaaattgtatctcattacttgtttcacaagagagctatcatgtgctaatgtacttacttttgcatatt----cagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG
                                    ||       || || || || |||    |   |      |       |  |||           | | || || |  | | |||    || |||  |    ||||||||| |||| || || || || ||||| || |||||||||||||||||||| || || || ||||||||||| ||||| |||
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 15
gtgaacacgtagaatatactgtgtacataaaattgtatctcattacttgtttcacaa----gagagctat-catgtgctaatgtacttacttttg-catattcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG----------------
    | || || ||   |||   | |  |   ||   |||| ||| ||||     ||     || ||||  ||  |  |  | ||| |  ||||| | | |||||||||||||||||||||| || || ||||| || || ||||||||||| |||||| |||| || ||||  |  || |||||||||                
--ttatacataaaaagcact---tgcccagtctttcctctccttatttgtacagtaattattagtgctagacagttcattttttacctttttttgtcctgttcagAGAAATCTGATCCGTGAGGCAACAGCTTTTCTGCTAGATGTTCTGAAACCAAATCTACCAGAACATGGGTACCTTCAAACTAAGGTGTTGGAGATAAATC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 15
gtgaacacgtaga-atatactgtgtacataaaattgtatctcattacttgtttcacaagagagctatcatgtgctaatgtacttacttttg-catattcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG----------------
 |  |||   ||  |  | |   |  | |     |   | |  ||||     | |  |  |    |   |    | ||   |||  ||||| | | |||||||||||||||||||||| || || || || || || ||||||||||| |||||| |||| || ||||  |  || ||||| |||                
-tctacataaaggcaccttcccagatctttcctctccttatttttacagtaattattattgctagacagtacatttattaccttttttttgtcctgttcagAGAAATCTGATCCGTGAGGCAACAGCCTTTCTGCTAGATGTTCTGAAACCAAATCTACCAGAACATGGGTACCTTCAAACAAAGGTGTTGGAGATAAATC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 15
-------------------------------gtgaacacgtagaatatactgtgtacataaaattgtatctcattact---tgtttcacaagagagctatcatgtgctaatgtacttacttttgcatattcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG
                                |||| |   | |  ||| | | |      |    |   | | ||||   || |||   | |    | | || | | | | |  |||||||    |  |||||||||||||||||| || || || ||||| || ||||||||| | ||||||||| |||| || ||||  || || || || |||
gttgattatatgttgtgattaagcaattatgatgaatattaatatgatattttttttcatgatcattgatttagtactgaatggttcttgaaattattgttattttc-attttggttactttc---tgctcagAGAAATCTGATCCGAGAGGCTACAGCTTTTCTCCTGGATGTTTTAAAGCCAAATCTACCAGAACATGGGTTCCTTCAGACAAAG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 15
gtgaacacgtagaatatactgtgtacataaaattgtatctcattacttgtttcacaaga--gagctatca--tgtgctaatgtacttacttttgcata-ttcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG
|||| || |    |||    |  |  | |  ||||    || || |   || ||  |     |  || ||  |  ||| | ||  ||| | ||| ||  ||||||| ||  |||| |||||||| || || ||  |  | |||||| |||||||||||||||| ||||||| ||| |||||||| |||
gtga-catgcttcata---ggactgaacagtattgggcatcgttgcaatttgcaagatgccaaattaccaattaagcttaagtctttattattgtattcttcagAGGAACTTGATACGTGAAGCAACAGCATTTTTGTTAGATGTTTTGAAGCCAAATTTACCTGAGCATGGTTTCCTGCAAACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtttcacaagagagctatcatgtgctaatgtacttacttttgcatattcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG
                                  tacttac  putative branch site (score: 1)
                                        cttttgc  CT-rich tract
                                     ttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaacacgtagaatatactgtgtacataaaattgtatctcattacttgtttcacaagagagctatcatgtgctaatgtacttacttttgcatattcagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC