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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG

Basic information

species Arabidopsis thaliana
transcript AT5G59850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
    |||   ||| |    |  | || ||   ||   |||| | |   ||| |||||| |  |   |  ||| ||    ||| ||| |  |  |  |||||||||||| ||||| |||||||| |||||||||||  |||| ||||||||||| ||||| ||||||||||| || |||||||| || || || || ||
----gttagccctcc----tcaaccttatgccca---tttgaattg--cttcattctgaggatacgcccctgatt----attattgttctatat-tagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 2
gtatgttgatcctgcattgtttagctcattttcacattttg--taataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
                    ||||| |   |  || || ||   | |    ||| |||  | |  |   |  |   | |  ||| ||| |  |  |  ||| |||||| | ||||| |||||||| |||||||||||  |||| ||||||||||| ||||| ||||||||||| || |||||||| || || || || ||
-------------------gttagccctcctcaaccttatgcccatttgaattgcttcattctgaggatacgtccctgattattattgttctatat-tagGCTACATTAGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G177720_T01 (Zea mays), 3'ss of exon 1
gtatgttgatcctgcattgtttag--ctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttt-taacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
                ||   |||  |||    | |     |||   ||   ||| ||  | |  ||  |  |||   | |   || || ||  | || ||| |||||||| ||||| |||||||||||||||||| | || || |||||||||||||| || || || || || ||||| || || |||||||| |||||
---------------gttagctagcactcgaccttatgccctgtttcaa---tgactccat-tccgaggacatgtccatgatcattgtgctgtta-tgtagGCTACATTGGAGAGTTCGAGTACGTTGATGACCACCGATCGGGCAAGATCGTGGTCGAACTCAACGGGAGGCTGAACAAGTGCGGCGTCATCAGCCCTCG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G083497_T04 (Zea mays), 3'ss of exon 1
gtatgttgatcctgcattgtttagctcattttcacattttgtaataacctt-gattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
    |||  | ||  ||    |  | |||||   || || | |  |  |   |  |  ||   |||| |  || | ||  |||              ||| |||||||| ||||| |||||||| |||||||||||  |||| ||||| ||||| || || || || ||||| |||||||| || || || || || ||
----gttagttctcaatctcgtgccccattt---caattggcagcattccgaggatacgtacctgattag-tgctatattatt--------------agGATACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATTGTGGTGGAACTGAACGGCAGACTAAACAAATGCGGTGTAATTAGCCCCCG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S426_18V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtt--tgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
   | | |   ||   |||     |    |   | |  | |  |     |   | | | |  ||  |     |  |||||  |  |||||       | ||||||| ||||| |||||||||   |||||||||||| |  |||| ||||| ||||| ||||| ||||||||| | ||||| || || ||||||||||||||
ctctctctctctctctcatctacgaaaataaact-atttatcttcgcgtctaagttgcagcattgatagcggatcgttttctctcttttggctct-tttcagGTTATATTGGAGAGTTTGAGCTTGTTGATGACCACCGAGCTGGCAAGATTGTGGTAGAGCTCAATGGAAGATTGAACAAGTGCGGTGTCATCAGTCCTCG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S41_94V6.2 (Physcomitrella patens), 3'ss of exon 2
------gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
       ||  || |      | |||  |    || |  |  |   || | |   |||| | |    ||  |    |||| | | |  ||   |     |||||| |||||||| ||||||||    || |||||||||||  | || ||||| || || ||| | || |||||||||||||| || ||||| |||||||||||
tttgttttaatttaacttgaaactgtcgaaaagatct--atgtcgagtcacacaattgaatttagagttt-tggtttgttctta-accttaccttcgtttgcagGCTACATTGGCGAGTTTGAACTGGTAGATGACCACAGAGCAGGCAAGATTGTTGTTGAGTTAAACGGAAGACTTAACAAGTGCGGAGTTATCAGTCCTCG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ26253 (Selaginella moellendorffii), 3'ss of exon 1
gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
                                        |||| | | | |   |    |    |     ||||   |||  ||  |    |  |||| ||||| || ||||||||||  || || || ||||| || || |||||||| |||||||| || || || || ||||| |||||||||||||| || ||
----------------------------------------gtaagatcttcg---cgaattccttttggtcgtttcttcatcctt--ttgcgcatcagGCTACATCGGCGAGTTTGAGTGGGTCGACGATCACAGATCCGGGAAGATCGTCGTCGAGCTAAACGGCAGGCTCAACAAGTGTGGAGTCATCAGCCCGCG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 1
gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
                                        |||| | | | |    |   |||  |    |||||   |||  |   |    |  |||| ||||| || ||||||||||  || || || ||||| || || |||||||| |||||||| || || || || ||||| |||||||||||||| || ||
----------------------------------------gtaagatcttcgcgaattccttt--ttggttgtttcttcatcctc--tcgcgcatcagGCTACATCGGCGAGTTTGAGTGGGTCGACGATCACAGATCCGGGAAGATCGTCGTCGAGCTAAACGGCAGGCTCAACAAGTGTGGAGTCATCAGCCCGCG

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|152037907|gb|BP802584.2|BP802584
EST:     GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACG                         GTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
genomic: GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACGgtatgttgat ... gaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
EST: gi|86080051|gb|DR375808.1|DR375808
EST:     GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACG                         GTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
genomic: GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACGgtatgttgat ... gaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
EST: gi|125213058|gb|EL227981.1|EL227981
EST:     TCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACG                         GTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
genomic: TCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACGgtatgttgat ... gaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
EST: gi|86052270|gb|DR348027.1|DR348027
EST:     GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACG                         GTTACATTGGTGAGTTTGAGTACGTTGATGACGACAGGTCTGGAAAGATCG
genomic: GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACGgtatgttgat ... gaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
EST: gi|86081708|gb|DR377465.1|DR377465
EST:     GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACG                         GTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
genomic: GCCTTCCTCTAAAGTGATCATCAAGTTTCTTATCGTCATGCAGAAACACGgtatgttgat ... gaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
EST: gi|125054014|gb|EL124898.1|EL124898
EST:     TGCAGAAACACG                         GTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG
genomic: TGCAGAAACACGgtatgttgat ... gaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG
                             ttttaacatttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG