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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatagagatacaacattggattttctatccacctggttgatgttcagcttttgcctccaattaacgttcttctgctctattcgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG

Basic information

species Arabidopsis thaliana
transcript AT1G14400.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 4
-gtaagttatagagatacaacattggattttctatccacctggt--tgatgt-tcagcttttgcctccaattaacgttcttctgctctattcgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG
 |  | || |   ||  ||    || |  ||  |    | || |  || ||| ||  | ||||  |    ||       || | || |  || | ||  ||||||||| |||||||| || ||||| || || ||||||||||||||||| || || |||||||| ||||||||||| || |||||||||
tgctacttgtgtggaagcacttatgtaccttagaatagcatgatattgttgtatctccatttgttttactttcctaacattttccttttatcat-gtacagTTTATGCTGATGGGAGCATATGCTTAGATATACTACAAAACCAGTGGAGCCCCATATATGATGTAGCTGCTATACTCACATCCATCCAG

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------gtaagttatagagatacaacattggattttctatcca-------cctggttgatgttca-gcttttgcctcca-attaacgt----tcttctgctctattcgt-------tgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG
                                                             ||||    ||    | ||      |||||| |       |  ||   ||  | |   | |||  |||| |||| | |    |||    ||  ||| ||       ||   ||||||||||||||| ||||| |||||||| ||| |||| || ||||||||||| || |||||||| || |||||||| || |||||||||
gtatgtcacaatcctattcttgaattgcattcctggttatgcaatatagatcataaactgcttatgcgaatgtttctttttggcatctatctattactctctaggactatactaacaatgttgtttccacattagcatctaatctctgactgcatttgtatgggtttgatcagTTTATGCAGATGGAAGTATTTGCTTGGATATTTTACAGAATCAGTGGAGTCCTATATATGATGTGGCAGCTATACTCACTTCCATCCAG

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
----gtaagt---tatagagatacaacattggattttctatccacctggttgatgttcagct--tttgc-----ctccaatt--aacgttcttctgctctattcgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG
    | | |    |      |  |  ||  |  |       || ||      |   |||||   | |||     || ||  |  |||     |   | | ||  |  ||| ||| ||||| || ||||| || ||| ||||||| || ||||||||||||||||| ||||| || ||||| || || || || || ||||||
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgc-gtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG

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|124950182|gb|EL025665.1|EL025665
EST:     TCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
genomic: TCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
EST: gi|125081392|gb|EL142632.1|EL142632
EST:     CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATCT
genomic: CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATCT
EST: gi|164028319|gb|ES000614.1|ES000614
EST:     CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATC
genomic: CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATC
EST: gi|124966115|gb|EL040241.1|EL040241
EST:     AATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATTTGCTTGG
genomic: AATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGG
EST: gi|86077068|gb|DR372825.1|DR372825
EST:     CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
genomic: CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
EST: gi|301501590|gb|HO207130.1|HO207130
EST:     CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
genomic: CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
EST: gi|47831557|gb|CK121241.1|CK121241
EST:     CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
genomic: CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTC
EST: gi|125254412|gb|EL268497.1|EL268497
EST:     CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATA                         TTTATGCAGATGGGAGTATCTGCTTGG
genomic: CAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttata ... cgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgttcagcttttgcctccaattaacgttcttctgctctattcgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG
                      aattaac  putative branch site (score: 2)
                              ttcttctgctctattc  CT-rich tract
                      aattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatagagatacaacattggattttctatccacctggttgatgttcagcttttgcctccaattaacgttcttctgctctattcgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT