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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgggataggcagttaatgaaaatcagcgtgttgctttggatgttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG

Basic information

species Arabidopsis thaliana
transcript AT2G07050.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 9
--gtttgggataggca-gttaatgaaaatcagcgtgttgctttggatgtt---cttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG
  |  ||    | ||| |||     | |  |   |  |  |    || |    |  |  | |  | |   |||  |||||      | ||||  | || ||||||||||||||||| | | | ||||| |||||||| |||||||| || ||||| || || ||||| ||||| |||||||| || || |
gtgcatgcctcatgcatgttcccttatacgattatactaatcaacatttcaagccatctcattacttacctgtggcttttatcctgaaagGTTATCGATGACTGCCCTGGAGATCTTAGTCAGTGGTACCGCCACATATCTAAAGGTGCATGGCCCTTTTCTACTGCTGATCATGGTTGGCCTATATCAG

upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 7
gtttgggataggcagttaatgaaaatcagcgtgttgctttggatgttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG
||   |   |      |  |   |   |  ||      || | |    ||    | || || | ||  | |||  ||   | ||||  | || ||||||||||| ||||||||| ||||||| |||||||  |||||||| || ||||| ||||||||||| ||||| |||||||| || ||||
gtacagtcgacatgcctttttgtatatattgttcaatcttaggttcatttacagcactgataaatggctgttta-atatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG

upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 9
gtttgggataggca--gttaatgaaaatcagcgtgttgctttggatgttcttttccct-ctcatgattgtttcttt-tcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG
     | | || ||   |   |     ||    || | |  |    || |||| |  | || || | ||| | ||| |||||  | ||||  | || ||||||||||| ||||||||| ||||||| |||||||  |||||||| || ||||| ||||| || || ||||| |||||||| || ||||
-----gtacagtcaacatgcctttttgtctatatggttcaatcttagtcctttacattactgataaatgtctatttatcatg--aaagGTTCTTGACGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGCGCATGGCCATTCTCCACCGCGGATCATGGTTGGCCTATATCTG

upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G00430.1 (Glycine max), 3'ss of exon 10
gtttgggataggcagttaatgaaaatcagcgtgttgctttggatgttcttttccct-ctcatgattgtttcttttcatggtata---gGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG
           |   |   |   | | | | | ||   ||| ||   |||  || |  | || ||| ||| | ||  | || ||   ||| |||||||| || || || ||||| ||| | ||||| || |||||||| ||||| ||||||||||| ||||||| |||||| || ||||| || ||||
-----------gtgttcttttgcatttatcattttaagttgcattgacttgcccttgttgataattttttttcttttttgtttaaaagGTTTTAGAAGATTGTCCAGGTGATCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTG

upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------gtttgggataggcagttaatgaaaatcagcgtgttgctttggat--gttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG
                          ||| | |    |  | | | | |   |  ||  | |    | |   |  |||||   ||  || |||  | || |     |  |||| |||||||| || || ||  ||||  |||| ||||||||||||||||| ||||| ||||||||||| ||||| |  ||||| || ||||||||||| |
gtgctttcatcacttattgggatttatttagaactttc--taatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaatgttgt-----tgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG

upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------gtttgggataggcagttaatgaaaatcagcgtgttgctttggatgttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG
                   ||    ||      ||| |  || |||   | ||  | |   | ||  || | ||  ||    | ||     |     |  |||||  |||||| |  || || ||| ||   ||||||||||| || ||||||||||| ||||||||||| ||  |   ||| ||||| ||||| |||||||
aacgtcgtgagtgtgtactttctaaatgtttgtttactttaattcacaatatt--tgttagtattagttgcacttacagagattttaaacgtgtctctgaagGTGAGAGAAGATTCTCCAGGGGATATGGCCTACTGGTATCGTCATATTTCTAAAGGTGCTTGGCCTTTTTCTTCAAGAGACCACGGATGGCCTATCTCTG

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|124952633|gb|EL027888.1|EL027888
EST:     GGCCCGTTTTGGAAAAAGCACATTCATTTGTCAAGAATTCCCAG                         GTGTTAGAAGACTGCCCT
genomic: GGCCCGTTTTGGAAAAAGCACATTCATTTGTCAAGAATTCCCAGgtttgggata ... catggtatagGTGTTAGAAGACTGCCCT
EST: gi|125123374|gb|EL169823.1|EL169823
EST:     AATATGGGCCCGTTTTGGAAAAAGCACATTCATTTGTCAAGAATTCCCAG                         GTGTTAGAAGACTG
genomic: AATATGGGCCCGTTTTGGAAAAAGCACATTCATTTGTCAAGAATTCCCAGgtttgggata ... catggtatagGTGTTAGAAGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgttgctttggatgttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG
                ttcttttccctctcat  CT-rich tract
                                     tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgggataggcagttaatgaaaatcagcgtgttgctttggatgttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA