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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttcatgttatctacctcgatgcaaagcggttttcttatgttcctcataaatgctaatacttgcttgcacatgttttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTCTTGACATTGTTCTACACTG

Basic information

species Arabidopsis thaliana
transcript AT5G41600.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G41600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g00640.t01 (Vitis vinifera), 3'ss of exon 3
-gtattgttcatgttatctacctcgatgcaa----agcggttttcttatgttcctcataaatgc------taatacttgcttgcacatgtt-----ttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTCTTGACATTGTTCTACACTG
| ||| | | || |||| ||| || | | ||| || | | | || | | | ||||| | || ||| | |||| ||||||||||||||||| |||| ||| | ||||| || | ||||||||||| |||||||||| |
agcattcctagttccatataccatgatttaatgtaaactgttatcatttttagatcgtgttttcacaatgtaatatgggaatggtgctgtgattaatcagGTGATTGCTGGCTTGTGGGTGGTGTCAATTGTGGGCAGTTGGTGTAACTTCTTGACCTTGTTCTACATAG
















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|125110132|gb|EL162242.1|EL162242
EST:     CCCTTCTTAGGAACATTGCATCAGGAAAAGATGTCAAGAAATTTATCCTG                         GTAATTGCTGGCTTG
genomic: CCCTTCTTAGGAACATTGCATCAGGAAAAGATGTCAAGAAATTTATCCTGgtattgttca ... catgttttagGTAATTGCTGGCTTG
EST: gi|164100363|gb|ES203212.1|ES203212
EST:     CAAGAAATTTATCCTG                         GTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTC
genomic: CAAGAAATTTATCCTGgtattgttca ... catgttttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTC
EST: gi|164040359|gb|ES134264.1|ES134264
EST:     GAAATTTATCCTG                         GTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTC
genomic: GAAATTTATCCTGgtattgttca ... catgttttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTC
EST: gi|86075888|gb|DR371645.1|DR371645
EST:     CCCTTCTTAGGAACATTGCATCAGGAAAAGATGTCAAGAAATTTATCCTG                         GTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTC
genomic: CCCTTCTTAGGAACATTGCATCAGGAAAAGATGTCAAGAAATTTATCCTGgtattgttca ... catgttttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTC
EST: gi|124779678|gb|EH869621.1|EH869621
EST:     CCCTTCTTAGGAACATTGCATCAGGAAAAGATGTCAAGAAATTTATCCTG                         GTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGG
genomic: CCCTTCTTAGGAACATTGCATCAGGAAAAGATGTCAAGAAATTTATCCTGgtattgttca ... catgttttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcggttttcttatgttcctcataaatgctaatacttgcttgcacatgttttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTCTTGACATTGTTCTACACTG
                           tgctaat  putative branch site (score: 2)
 ttttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttcatgttatctacctcgatgcaaagcggttttcttatgttcctcataaatgctaatacttgcttgcacatgttttagGTAATTGCTGGCTTGTGGGTTTTGTCCATTATTGGCAGCTGCTACAACTTCTTGACATTGTTCTACACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT