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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattcccgatctcctccgatccaatttcgaaattgttggtttctagatttgaatttttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA

Basic information

species Arabidopsis thaliana
transcript AT5G42000.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 3'ss of exon 1
------------gtattattcccgatctcctccgatccaattt--cgaaattgttggtttcta--gatttga-attt--ttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
            | ||| |        |    | ||   ||     || |      || || |  |||||   | ||  | || |  | || | ||  || |||| || || |  ||||||||||||||||||||||| ||||  ||||| || ||| | || || | ||||||||||||||| || || || |||||||
actattctctttgcattttcgttagcatttctctatagcatcggatgatacctaccgtgtccaatgatttcccacttaatcgaataatcttatgtttcagATCACATACCACTTTTTCCATTGGAAGAAGGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAGCAAATGGACAATGGCA

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
------------------gtattattcccgatctcctccgatccaatttcgaaattgt-tggtttctagatttgaatttttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAG---ATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
                   ||  |||     ||  |  |  ||   |      | |   |  | | |  |  | ||||||    |  |||| |||   || |||| ||||| | ||||||||||||||||||||| |||||||  |   |||| |||||  |||| || ||| | |||||||||||||| |||||||| |   
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
------------gtattattcccgatctcctccgatccaatttcg-----aaattgttggtttcta--gatttgaatttttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
              |  |      |   | |  ||| |||||        ||  | ||  |  |||  |        |  | | |   |||   ||  || | || || ||||  || || |||||||||||||| || ||||  ||||| || ||  | ||||||||||||||||||||||| || || || ||||| |
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaactgaattttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
---------gtattattcccgatctcctccgatcca-atttcgaaattgttggtt-tctagat-----ttgaatttttgagttt---ttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
           ||||   ||  |    || | |  | ||||    || |    || || | ||     |||   | | || | |   |  | ||||  || |||| || || |  |||||||||||||| |||||||| ||||  ||||| || ||| | || || | |||||||||||||||||| || || |||||||
gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
-----------gtattattcccgatctcctccgatccaatttcgaaattgttggtttctagat-----ttgaatttttgagttt---ttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
           | ||| |     |    ||   |  || ||    ||       | || ||||     |||   | | || | |   | || ||||  || |||| || || |  |||||||||||||| |||||||| ||||  ||||| || ||| | || ||   ||||||||||||||| || || ||||||||||
tttggtttcttgaattttcatgtactatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA

upper sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G558324_T01 (Zea mays), 3'ss of exon 2
-----------gtattattcccgatctcctccgatccaatttcgaaattgttggtttctagat-----ttgaatttttgagttt---ttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
           | ||| |     ||   ||   |  || ||    ||       | || ||||     |||   | | || | |   | || |||| ||| |||| || || |  |||||||||||||| || ||||| ||||  ||||| || ||| | || ||   |||||||||||||||||| || ||||||||||
tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA

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|125261111|gb|EL275196.1|EL275196
EST:     ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTT
genomic: ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTT
EST: gi|124906820|gb|EH980900.1|EH980900
EST:     ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCAT
genomic: ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCAT
EST: gi|125225328|gb|EL239413.1|EL239413
EST:     CTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGAT
genomic: CTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGAT
EST: gi|125178960|gb|EL197081.1|EL197081
EST:     ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACC                         GTCACGTATCATTCCTTCCATTGGAAGAAGGG
genomic: ATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcc ... tgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcgaaattgttggtttctagatttgaatttttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
                                       tttttttgttttct  CT-rich tract
                        atttgaatttttgagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattcccgatctcctccgatccaatttcgaaattgttggtttctagatttgaatttttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG