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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgtttttctaaatcaaaactcggttcagacttcagctacaaactctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT

Basic information

species Arabidopsis thaliana
transcript AT5G53120.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G060896_T02 (Zea mays), 3'ss of exon 8
gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgttt-ttctaaatcaaaactcggttcagacttcagctacaaactctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT
  | || | || |||  |  | ||   || ||  |  || | ||    | |    | | | |||||    |  ||| |  | |  |      ||| |     | |||    ||  |   ||| |||||||  |  ||||| ||||||||||| || || ||| | |||||||| |||| |||||| || |||||||||||    || || ||||||||| |
--acgaataatttgctcatatttt---atttcaaaaagaattttgacctataaacttttagtcaaa----gactcaaatcttattt------tcttag----ttacttggcat--ttgcagGGCCTGCTCAGGAACTTGTAGAGAAGCCTTTTTTTGATACAATTGCTAGAGCTTTGAGGCCTGGAGGCGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 7
gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgtttttctaaatcaaaactcggttcagacttcagctacaaactctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT
 ||||||      | |||| |    |  | |    |        | || |  |      ||||||| |    ||| |  | |       | ||| | |||  || |    ||  |   ||| |||||||  |  ||||| ||||||||||| || |||||  | |||||||| |||| |||||| || |||||||||||    || || ||||||||| |
-tatgat------gaaaaatttgcagatttttcttgcagaaaggacttcgactc-----atcaaaatttcaatcaaatcttact-----attcttatgttg-catttggcat--ttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 8
gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgtttttctaaatcaaaactc----ggttcagacttcagctacaaactctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT
                     |||   | ||   | | || || |     | |    | || || | ||      ||  |         |  |||| | ||    | ||| | | ||||  |||||||||| |  |  |||||||||||||||||||| || ||| | ||||| || || | ||| || |||||||||||||| ||||||||||||||||||||
---------------------cttactacatgctaatcatactgaaag-atgtaaagagataaagattcctcaatttttggtcattatcattaactattacaggattacttt-tgtaatt-tagGTCCTGCCCAGGAACTTGTTGAGAAGCCTTTCTTTGATACAATAGCTAGGGCATTAAGGCCCGGTGGAGTTCTTTGTAATATGGCAGAAAGTATGTGGCT

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 8
gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgtttttctaaatcaaaactcggttcagact-tcagctacaaact-ctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT
                  || ||    ||| |  |   |||   |  ||    |||    || |   | ||||   | | | |   || ||||  | ||    ||| | | |   ||  |||||||||| |  |  ||||||||||| ||||| || || ||| | ||||| ||  | | |||||| |||||||||||||| ||||||||||||||||||||
-----------------cacgctaattataccaaaagaattaagagattaagattcc---tctatttttggttattattattattaactaactatttacaggatcaattt-tgcgatt-tagGTCCTGCCCAGGAACTTGTTGAGAAACCTTTTTTTGATACAATAGCTAGGGCACTAAGGCCTGGCGGAGTTCTTTGTAATATGGCAGAAAGTATGTGGCT

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 8
gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgtttttctaaatcaaaact-cggttcagacttcagctacaaactctcacgttttcactctatataatcat--agGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT
                 |||| |||   | |   ||       | |  | |     ||| |   |  |  ||   | |    |  ||   |||  |    |||   |   | |  ||||  |||||||||||  |  ||||| ||||  || || || ||||||   || ||||| |||   ||||| || ||||||||||||||||| ||||| ||||||||
-----------------aactttttatgtcttcaagg------tgtaatatcccaataagtgggatttgtggcaaataaggtaattatttacttcccttgtttggtttcttttcctcatttagGTCCTGCTCAAGAACTTGTCGAGAGACCATTTTTTGAGACAACAGCCAGAGCTTTGCGTCCTGGTGGTGTTCTTTGTAACATGGCTGAAAGCATGTGGCT

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|125295707|gb|EL309792.1|EL309792
EST:     CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG                         GTCCTGCTCTTGCGCTTGTTGAGAAGCCTTT
genomic: CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAGgtatgattca ... ataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTT
EST: gi|47829276|gb|CK118960.1|CK118960
EST:     CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAN                         GTCCTGCTCTTGCGCTTGNTGAGAAGCCTTTCTTCGAGACACTGGC
genomic: CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAGgtatgattca ... ataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGC
EST: gi|86080625|gb|DR376382.1|DR376382
EST:     CCYTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG                         GTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG
genomic: CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAGgtatgattca ... ataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG
EST: gi|164173473|gb|EL999811.1|EL999811
EST:     TGATGCCATCATTGTTGATTCTTCAGATCCCGTAG                         GTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG
genomic: TGATGCCATCATTGTTGATTCTTCAGATCCCGTAGgtatgattca ... ataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG
EST: gi|86079304|gb|DR375061.1|DR375061
EST:     CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG                         GTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG
genomic: CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAGgtatgattca ... ataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG
EST: gi|47831735|gb|CK121419.1|CK121419
EST:     CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG                         GTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG
genomic: CCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAGgtatgattca ... ataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcggttcagacttcagctacaaactctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT
                         ctctcac  putative branch site (score: 3)
                                        tctatataatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgtttttctaaatcaaaactcggttcagacttcagctacaaactctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC