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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattgatcttatcgacatacaatctcttaagctttatttgagcagattatgccattgttgcttttgcttgtagtaacagagataaattttatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGATTACCCGGAGAAACCTCCAACTGTCCGATTCCATTCACGTGTCAACATGG

Basic information

species Arabidopsis thaliana
transcript AT3G52560.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G027378_T01 (Zea mays), 3'ss of exon 2
-gcattgatcttatcgacatacaatctcttaagctttatttgagcagattatgccattgttgcttttgcttgtagtaacagagataaattttatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGATTACCCGGAGAAACCTCCAACTGTCCGATTCCATTCACGTGTCAACATGG
    | | |||| || |   |||      |    |  ||      |  |        | |    |||| ||  |    ||   | |  || | | |  |||||||| ||||| ||| | ||||| ||| ||||| | |||||||||||||| || |||||||| || ||| ||||| ||||||| ||| |  |||||||| 
tctgtaggtcttctctaacaacagcgcagtcttttccatagagttacttctcttggctatctaatttgtttccacgtccaacaacat-ttctctttgtcagACTGTACATGAGGGTCGCATCTACCAGCTGAAGTTGTTTTGTGACAAAGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGA

upper sequence: AT3G52560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G071010_T01 (Zea mays), 3'ss of exon 2
-gcattgatcttatcgacatacaatctcttaagctttatttgagcagattatgcca-ttgttgcttttgcttgtagtaacagagataaattttatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGATTACCCGGAGAAACCTCCAACTGTCCGATTCCATTCACGTGTCAACATGG
    | | |||| || |   |||     ||    |  ||  |||  | || |      | |    |||  ||  |    |  | |  | || | | |  |||||||| ||||| ||| | ||||| ||| ||||| | ||||||||||| || || |||||||| || ||| ||||| ||||||| ||| |  |||||||| 
tctgtaggtcttctctaacaacagcgcattcttttccata-gagttgcttctcttggctatctaatttatttcca-cgtcccacaacatttctctttgtcagACTGTACATGAGGGTCGCATCTACCAGCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGA

upper sequence: AT3G52560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 2
---gcattgatcttatcgacatacaatctcttaagctttatttgagcagattatgccattgttgcttttgcttgtagtaacagagataaattttatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGATTACCCGGAGAAACCTCCAACTGTCCGATTCCATTCACGTGTCAACATGG
      |||   ||     | ||     || |      | | |   || ||  |     |   | ||||   |  | ||||     ||| |  | | ||  || |||| ||||||||| | || |||||  ||||||| |||||||| |||||||| |||||||| ||||| | ||| || |||||||||||  |||||||| 
aagattttgtgtttgatagcttattccatcgtgtatcatgtattctcacatc-tatacatacagattttatgttcattaactattttaattactttttc--agTCTGTACATGAAGGTCGCATTTATCAACTGAAGCTTTTTTGTGATAAAGATTATCCGGAGAAGCCTCCTAGTGTACGGTTCCATTCACGCATCAACATGA

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|86018900|gb|DR314646.1|DR314646
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018875|gb|DR314621.1|DR314621
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018902|gb|DR314648.1|DR314648
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018872|gb|DR314618.1|DR314618
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018874|gb|DR314620.1|DR314620
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC---                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018885|gb|DR314631.1|DR314631
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTT-TGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018891|gb|DR314637.1|DR314637
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTA                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018896|gb|DR314642.1|DR314642
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTA                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018898|gb|DR314644.1|DR314644
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCYCACAAC--A                         -CTGTYCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|164043829|gb|ES081846.1|ES081846
EST:     ACTGGCACCATCATCGGTCCTCACAACGTA                         GCTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018881|gb|DR314627.1|DR314627
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC---                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018878|gb|DR314624.1|DR314624
EST:     ACATCTATATGCGTTCTTGGACTGGCACTATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018884|gb|DR314630.1|DR314630
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTA                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018901|gb|DR314647.1|DR314647
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018887|gb|DR314633.1|DR314633
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018871|gb|DR314617.1|DR314617
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018880|gb|DR314626.1|DR314626
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTA                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAG
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAG
EST: gi|86018883|gb|DR314629.1|DR314629
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018899|gb|DR314645.1|DR314645
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018895|gb|DR314641.1|DR314641
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018882|gb|DR314628.1|DR314628
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTA                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018873|gb|DR314619.1|DR314619
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC--A                         -CTGTTCATGAAGGTAGAATCTATAAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatgccattgttgcttttgcttgtagtaacagagataaattttatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGATTACCCGGAGAAACCTCCAACTGTCCGATTCCATTCACGTGTCAACATGG
                          tagtaac  putative branch site (score: 1)
                                 agagataaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattgatcttatcgacatacaatctcttaagctttatttgagcagattatgccattgttgcttttgcttgtagtaacagagataaattttatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGATTACCCGGAGAAACCTCCAACTGTCCGATTCCATTCACGTGTCAACATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA