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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattcttctttctgacgtaattaacaaaaaagatgatgaagataatgaaataattaaaaactcatggcctaattaggttgatttaatatcttgatgagaatttctgtatacgcaaatttgtttcctttttcatagaagaaagtgtggtaactgattattgtgtgtggttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGACAACTACATCAACTACCACAAGCGTTTGATCGATCTTGTGAAAATTGGAG

Basic information

species Arabidopsis thaliana
transcript AT4G34050.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34050.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G33780.2 (Glycine max), 3'ss of exon 4
gtaagcattcttctttctgacgtaattaacaaaaaagatgatgaagataatgaaataattaaaaactcatggcctaattaggttgatttaatatcttgatgagaatttctgtatacgcaaatttgtttcctttttcatag-aagaaagtgtggt-aactgattattgtgtgtggttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGACAACTACATCAACTACCACAAGCGTTTGATCGATCTTGTGAAAATTGGAG---
                                                                                       |  ||       | | ||| |     ||   |||       |  ||     || || |||| ||  |    |  | ||||||||||||    |||||||||||||||||||||  |||||||| || || |||||||| ||||| ||||||||| |||||||||||||| | ||||| || ||||| ||| |||| |   
---------------------------------------------------------------------------------------tctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcaggagAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGGGCG

upper sequence: AT4G34050.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
gtaagcattcttctttctgacgtaattaacaaaaaagatgatgaagataatgaaataattaaaaactcatggcctaattaggttgatttaatatcttgatgagaatttctgtatacgcaaatttgtttcctttttcatag-aagaaagtgtggt-aactgattattgtgtgtggttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGACAACTACATCAACTACCACAAGCGTTTGATCGATCTTGTGAAAATTGGAG
                                                                                     |||  ||       | | ||| |     ||   |||       |  ||     || || |||| ||  |    |  | ||||||||||||    |||||||||||||||||||||  |||||||| || || |||||||| ||||| ||||||||| |||||||||||||| | ||||| || ||||| ||| |||| |
------------------------------------------------------------------------------------aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG

upper sequence: AT4G34050.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G11530.1 (Glycine max), 3'ss of exon 4
gtaagcattcttctttctgacgtaattaacaaaaaagatgatgaagataatgaaataattaaaaactcatggcctaattaggttgatttaatatcttgatgagaatttctgtatacgcaaatttgtttcctttttcatagaagaaagtgtggtaactgattattgtgtgtggttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGACAACTACATCAACTACCACAAGCGTTTGATCGATCTTGTGAAAATTGGAG
                                                                          |||  |   ||    | | | |  || |     ||  || |    |||   |||        | | ||||  ||    |   |    |||| |||||||    ||||||||||||||||||| |  |||||||| || || || || || ||||| ||||||||| |||||||||||||| | ||||| || ||||| ||| |||| |
--------------------------------------------------------------------------taaaaaaaatg--caagtttttccatca----ctcaataaaaaataatcaatttagaggagta-aaaagagggta-attgggtagcgattgcgtgtggtgaaatgcagGAGAAGAACCATGGGAGCTATGACTTCATCTTTGTGGACGCAGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTCAAAGTTGGGG

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|116431209|gb|EG473801.1|EG473801
EST:     AGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: AGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
EST: gi|124767213|gb|EH857343.1|EH857343
EST:     ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGA
genomic: ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGA
EST: gi|125012543|gb|EL084812.1|EL084812
EST:     CCCTGCTCCTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: CCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
EST: gi|124923130|gb|EL001353.1|EL001353
EST:     ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGC
genomic: ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGC
EST: gi|116428558|gb|EG471150.1|EG471150
EST:     ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
EST: gi|125093528|gb|EL151079.1|EL151079
EST:     CTCTTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: CTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
EST: gi|164181633|gb|ES123865.1|ES123865
EST:     CTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: CTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
EST: gi|125164199|gb|EL190896.1|EL190896
EST:     TCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: TCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
EST: gi|125257471|gb|EL271556.1|EL271556
EST:     TTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: TTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
EST: gi|124962165|gb|EL036609.1|EL036609
EST:     ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTT
genomic: ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTT
EST: gi|124797423|gb|EH887102.1|EH887102
EST:     ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTG-C                         GAGAAGAACCATGGAACATATGACTT
genomic: ACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTT
EST: gi|124843660|gb|EH928097.1|EH928097
EST:     CCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC                         GAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC
genomic: CCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGACgtaagcattc ... ttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttttcatagaagaaagtgtggtaactgattattgtgtgtggttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGACAACTACATCAACTACCACAAGCGTTTGATCGATCTTGTGAAAATTGGAG
                             tgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcattcttctttctgacgtaattaacaaaaaagatgatgaagataatgaaataattaaaaactcatggcctaattaggttgatttaatatcttgatgagaatttctgtatacgcaaatttgtttcctttttcatagaagaaagtgtggtaactgattattgtgtgtggttgggtgcagGAGAAGAACCATGGAACATATGACTTTATATTCGTTGATGCTGACAAAGACAACTACATCAACTACCACAAGCGTTTGATCGATCTTGTGAAAATTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG