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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaattagatttgaattgtgttaaataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC

Basic information

species Arabidopsis thaliana
transcript AT1G21065.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G21065.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 4
gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaattagatttgaattgtgttaaataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC
                                                   ||  ||      | ||| |   || |   ||   | |||  |  ||||  |      ||| |     || | |       || | | |  ||   ||| | ||||   |||||| ||||||||||||||||| ||||| || |||||||||||||| |||   || ||
--------------------------------------------------ctagcatacggttttttgatttgttaagagtcaagactgtactattcttcag------atcaggccatattagtca----atagtcataactgtgctgt-tcaaat---tgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaattagatttgaattgtgttaaataatt-gcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC
                                                               | ||  |  | || |     |   |   | | |  | ||||  | | |   | ||||| ||  | | |  || |      ||||||      | ||| ||||| ||||||||||||||||| |||||||| |||||||||||||| |||   || | 
--------------------------------------------------------------ttattcatggcgttgtttataggtttcctacttttgtaggcag-agaccatgtatcatgcatgatttag--atcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaattagatttgaattgtgttaaataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC
                                                          ||    |||||| |  ||||    || ||||   | || || |||  |   | |    | || |  |   |  |  |  |||||| |||    | ||   ||||||| || |||||||||||||||||||| || ||||| |||||||| |||  ||||||
--------------------------------------------------------ataagtcagttgttac--ttattaagtgtaatgc--tgctgttaggctgttagttttccattataatatacatatttttctgatttggatt----tgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0122g00190.t01 (Vitis vinifera), 3'ss of exon 4
gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaat-tagatttgaattgtgttaaataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC
                                                        | | | || ||      |  ||  |   ||| |  |     |  |  |    |  || |   | ||| ||||    ||  | ||||  ||   ||   ||   || ||||||| |||||||||||||| || ||||| || ||||||||||| ||    |||||
--------------------------------------------------------tgacaaatattaga---taaatgataaaaaaggaaagcaaataagaga----aattgttcataagaagtttgccacaaaattgattctaaccctgc--aaccttttcagGTCCGGATGACATGCCAGCACACATCAAATCTTCAATGTTTGGTTGCAGTCTCAC

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|116377495|gb|EG420087.1|EG420087
EST:     GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTC
genomic: GGGAATTCAGCGCCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTC
EST: gi|86078659|gb|DR374416.1|DR374416
EST:     GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
genomic: GGGAATTCAGCGCCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
EST: gi|124795012|gb|EH884691.1|EH884691
EST:     GGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
genomic: GGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
EST: gi|125043447|gb|EL115716.1|EL115716
EST:     CCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
genomic: CCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
EST: gi|124735337|gb|EH826739.1|EH826739
EST:     AATTCAGCGCCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
genomic: AATTCAGCGCCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
EST: gi|116377317|gb|EG419909.1|EG419909
EST:     GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATAAAAGTTTGGATGTCAAC
genomic: GGGAATTCAGCGCCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
EST: gi|124709996|gb|EH801398.1|EH801398
EST:     ATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
genomic: ATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
EST: gi|125074573|gb|EL138462.1|EL138462
EST:     CCTGAGGGGAATTCAGCGCCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCA
genomic: CCTGAGGGGAATTCAGCGCCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCA
EST: gi|125239990|gb|EL254075.1|EL254075
EST:     CGCCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
genomic: CGCCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAAC
EST: gi|86028440|gb|DR324193.1|DR324193
EST:     GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG                         GTCCTGATGACATGCCAGCTCATATC
genomic: GGGAATTCAGCGCCTTGGAGGCATACTATGGAAGgttagttgtt ... ataattgcagGTCCTGATGACATGCCAGCTCATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatttcatgaattttgttgtaattagatttgaattgtgttaaataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC
 atctgat  putative branch site (score: 4)
                      taattagatttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaattagatttgaattgtgttaaataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA