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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattgagctttgtttttttcattcatggatttttcagttaattgtctgctgttccatgtttaattttcatcggtaaaagcttgctgttctgatgtttttctatggtgtttgtattgatttctgagagcagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTTTGTGAGGCAGTGGGTCCTGATTGCACGAG

Basic information

species Arabidopsis thaliana
transcript AT1G25490.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------gtgaat--tgagctttgtttttttcattc--atggatttttcagttaattgtctgctgttccatg-tttaattttcatcggtaaaagcttgctgttctg-atgtttttctatggtgtttgtat-tgatttctgagag---cagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTTTGTGAGGCAGTGGGTCCTGATTGCACGAG
                                                       || |||  | |   | ||     | | |    |    ||| ||    ||   || ||   | ||  ||| || | | |  ||   |||   ||    |  ||| ||    ||     |||  | || ||||| |      ||||||||||||||| | |||||||| ||||| || ||||| || |||||||| ||||| || || ||| ||||   ||| ||
gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactagagtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgttttcttaacatctcagGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgaattgagctttgtttttttcattcatggatttttcagttaattgtctgctgttccatgtttaattttcatcggtaaaagcttgctgttctgatgtttttctatggtgtttgtattgatttctgagagcagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTTTGTGAGGCAGTGGGTCCTGATTGCACGAG
                   ||   || |    | ||||||  |  |  |  | |    |||||   |    || | || |  | | |  |  | |  |  |      || |   | | |  |||      ||||| ||||| |||||||| || |||||||| || || ||| ||||||| ||||||||||| || || || ||    || ||
-------------------ttctgttaaatcttctttcag--agctaaccccaggg--atgttctttgagtatagttatatacatacaataattaaatcatg----agtttccctgtgggattc------cagGACAAATCATGGAGGGTACGATACATGGTGGCCAACCAGTTATATGAGCTTTGTGAGGCGGTAGGACCAGAACCAACCAG
















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|124917467|gb|EH991341.1|EH991341
EST:     TTTTACCTGTTATTGTTAATTTCTCTCAG                         GATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTT
genomic: TTTTACCTGTTATTGTTAATTTCTCTCAGgtgaattgag ... ctgagagcagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTT
EST: gi|86067631|gb|DR363388.1|DR363388
EST:     CTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGTTAATTTCTCTCAG                         GATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTT
genomic: CTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGTTAATTTCTCTCAGgtgaattgag ... ctgagagcagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTT
EST: gi|125069874|gb|EL135494.1|EL135494
EST:     ATTGTGTTGCACGCATTTTACCTGTTATTGTTAATTTCTCTCAG                         GATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAA
genomic: ATTGTGTTGCACGCATTTTACCTGTTATTGTTAATTTCTCTCAGgtgaattgag ... ctgagagcagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcttgctgttctgatgtttttctatggtgtttgtattgatttctgagagcagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTTTGTGAGGCAGTGGGTCCTGATTGCACGAG
                                    tattgat  putative branch site (score: 3)
                                          tttct  CT-rich tract
                   tttttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattgagctttgtttttttcattcatggatttttcagttaattgtctgctgttccatgtttaattttcatcggtaaaagcttgctgttctgatgtttttctatggtgtttgtattgatttctgagagcagGATAAATCTTGGAGGGTGCGCTACATGGTTGCTAATCAGCTATATGAACTTTGTGAGGCAGTGGGTCCTGATTGCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT