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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

Basic information

species Arabidopsis thaliana
transcript AT1G23260.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
-gaatgtgatcggatccatggtctc--gattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
    | |  | ||||     | |||  || ||| |  |||    |    |  | | |||   ||   |     | ||||   | |||   |       || |||||| || ||||||||| || | |||||||||||  |||||||||| || ||||| ||||| || || |||||||||||||||||||||||||| || ||
attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaat--tctttact-gtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
gaatgtg-atcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
   |||  |   || | ||||  | || |   |  ||| ||| | || |   ||  |     |      |||  |     |  ||    | | |  || |||||| || ||||||||  || | ||||| || ||| | |||||||| || ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||
ttttgttcacaagaacaatggatttgaattc-tgaatacctgttatgcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G022859_T01 (Zea mays), 3'ss of exon 1
gaatgtgatcggatccatggtctcgattaggtatatatctga---tctgtaaaatgatttgatttgggggcgatatttataagagcttgattt------tgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
        |    | ||    | | || |  |  |  |||||   ||||  |  | || |   |||      || |  || | |  ||| | |      | |  || |||||| || ||||||||  || | ||||| || ||| | |||||||| || ||||| ||||| ||||| |||||||| ||||| ||||||||||| || | 
--------ttttgttcacaagcacaatgaatttgaactctgaatatctgctat-tcatgttgcttgataataatttagatcatactttgttctatggcgttttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATT

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgat-tttgtg-atgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
 ||  |           || ||    || | | ||  | |  | | | ||||  ||  | ||||   | || ||   ||    ||  | | | || |||||||||| |||||||| ||||| |||||||||||||| ||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| ||
taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaat--ttgtaattggcacctatcttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
---gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgat-gtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
        |||| |  | |||  | |    ||  | | | | |  | |||||| |  | | |||||    | || ||  ||| |  ||   | | || | | |||||| ||||| || ||||| |||||||||||||| ||||||||||| || ||||||||||| ||||||||||| ||||||||||||||||||||||| ||
cttatcactgattgtgttcatcttttattgtaact-tcttttttttttgtaaatt--tgtaatttgcac-ctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G24950.1 (Glycine max), 3'ss of exon 1
gaatgtgatcggatccatggtctcgattaggt--atatatctgatctgtaaaat--gatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
 | ||   ||  |||  |  |    | ||  |  ||  | | | | || |  ||   ||   | || |    || |||||      ||| |||      || |||||| ||||| || ||||| |||||||||||||| ||||||||||| || ||||| ||||| |||||||||||||||||||||||||||||||| || ||
-attgccttc--atcagtcattgtaagtatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactctt-cttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaat--gatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
     | ||| |    || |   | |||     || | | | | || |  ||   ||   | || |    || |||||      ||| |||      || |||||| ||||| || ||||| ||| |||||||||| ||||||||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || || ||
tgccttcatcagtcatattgcaactatttcaattaaa-cagctttgaaggatttaatagaacttagatttgaaatttactctt-cttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 1
gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtg-----atgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
     |     |    ||  ||| | |   ||   ||  || ||| |  | || ||  ||     | |   |  ||||      ||||||||||     ||| |||||| ||||| || |||||  ||||||||||||| ||||| || || || ||||| ||||| ||||| || |||||||||||||||||||||||||| ||
----ttatcttggaaaattttctggttgttgttgctacatggtcttttgagtgcttgcatgcatag-caggagatatatctttgtgattttgtggtcatatgcagTTCCAAGGAATTTCAGATTACTGGAAGAGCTTGAGAGAGGGGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATA

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
--gaatgtgatcggatccatggtctcgattaggtatatatct-gatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
    |  | || | ||             |||   |||     | | ||      | |    ||  |  |   |||| |     | ||   ||      |||||||| ||||||||| |  |  | ||||| ||||| || || |||||||||||||| ||||| || || |||||||| ||||| |||| ||||||  | | 
gaagagttcatagaatgttgacatgtagctagtcgtatgctgaggtttgattctcgctccagttctgatg---tattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S311_60V6.1 (Physcomitrella patens), 3'ss of exon 1
---gaatgtgatcggatcca-tggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
    | | |   |   |  | | || ||   |||  |  |     || ||     || | |||||     |   ||    | | ||  |  | || |  || |||||| ||| ||||| |  |  | ||||| ||||| || ||||||||||| |||||||| || |||||||| ||||| ||||| || | ||| ||| | | 
tccaactttccacaatttgagtagtttcttctag--aactgctgcatttgcgtgttg-tgtgattccttagtcctacccttgatagtgtattgttatc-tgcagTTCCAAGGGACTTTCGTCTTCTTGAAGAACTTGAGAGGGGTGAGAAAGGAATTGGAGACGGGACTGTTAGTTATGGCATGGACGACGGTGACGATGTGTT

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
gaatgtgatcggatccatggtctcgatt---aggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtga---tgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
   | |  ||  || |     ||  |||      | |||||||||||  ||  |   | |  |||     |  |  || |||       | ||| |     | ||||||| ||||||||| |  |  | || |||||||| || |||||||||||||| || ||||| || || |||||||| |||||||| |  || ||| | | 
---ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttctttttt---ttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT

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|86060956|gb|DR356713.1|DR356713
EST:     TTATTCCTGAGATTCATCGGCGATGAGTTCGGAGGAAGCCAAGGTCGTTG                         TTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAAAAAGGTA
genomic: TTATTCCTGAGATTCATCGGCGATGAGTTCGGAGGAAGCCAAGGTCGTTGgtaagtctcc ... tgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTA
EST: gi|125071688|gb|EL136647.1|EL136647
EST:     TTATTCCTGAGATTCATCGGCGATGAGTTCGGAGGAAGCCAAGGTCGTTG                         TTCCGAGGAACTTTAGATTG
genomic: TTATTCCTGAGATTCATCGGCGATGAGTTCGGAGGAAGCCAAGGTCGTTGgtaagtctcc ... tgtgatgtagTTCCGAGGAACTTTAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
                                    gcttgat  putative branch site (score: 5)
                        atatttataaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - ctgatct
- - - - - - - - - - - - - - - - - - - - - - - -aaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgg