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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaagcattcttctacttgttctctgttcacaaaacgtagtcaaaaatttgcttgtgttgatatcactttcctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG

Basic information

species Arabidopsis thaliana
transcript AT5G53120.1
intron # 7
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 8
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 7
gtaa-ttaagcattcttctacttgttctctgttcacaaaacgtagtcaaaaattt---gcttgtgttgatatc--------------actttcctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG
 ||  ||  |  |||||   ||| || |   | || | |  || |      ||||     |||  || |||||               ||||  | | |||||||  || ||| |  | ||  ||||||||||||| |||||||| |||||||||||||| || || ||  | |
-tatcttgcgtgttcttaatctt-ttttgcatgcatatatggtggctttggattttaaaattgcctttatatcttcataatagacctgcttttattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G060896_T02 (Zea mays), 3'ss of exon 7
--------------------------------------------------gtaattaagcattc---ttctacttgttctctgttcacaaa-acgtagtca--aaaatttgcttgtgttgatatcacttt----cctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG
                                                   |  |  ||| |     ||||  | | | |  ||  | ||| ||  |||     || | |  ||        ||   |||    |  ||  ||||||  |||||| |  | ||  | ||||||||||  |||||||| |||||||||||||| ||||||||  |||
gtatgtagataattccatgaggctatgatgactacattattttctgatatatgctgtagcttcttgtttcttttagatattggtaaataaatactcagttcttgaactgtaatttcacaagaattgttttttatctactttcagCTGTGGAGTTCTTGAGAAATGCTCCTGAAGGGACATATGATGCTATCATTGTTGATTCGTCAGATCCAATAG

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 7
----------gtaattaagcattcttctacttgttctctgttcacaaaacgtagtcaaaaatttgcttgt---gttgatatcactttcctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG
           |      |  || || ||  | |  |    |  |      |   || || || | ||||    ||  |  |||     | || |||||| ||| || ||        |   ||||||||||||||||||||| ||||||||||| ||||||||||| |
gtatatatttatctgctggtcttgttttaaatttgtttgagttgcctcttctgtgcagaatttagtttgttaatttttttccacccatttttgacagCTGTTGAATTTCTTAAATCTGCTTGTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCCGTGG

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G13210.2 (Glycine max), 3'ss of exon 7
gtaattaagcat-tcttctacttgttctctgttcacaaaacgtag----tcaaaaatttgcttgtgttgatatcactttc-----ctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG
|||  ||   || |  |   |||||| |   ||   |  |  |      ||      ||   | ||||||| |   || |      | ||||||||| ||| || ||        | ||||||||||||||||||||||| ||||||||||| |||||||| || |
gtatatatttatctgctggtcttgttttgaatttgtatgagttgtctcttctgtggctttagtttgttgattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------gtaattaagcattcttctacttgttc-------tctgttcacaaaacgtagtcaaaaatttgcttgtg-----ttgatatcactttc----ctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG
                            |  ||    | || | |||  |           |   ||||       |  || || || |   |||      ||||| ||| ||||     | ||||||||| ||| || ||  |  |    |||||||||||||||||||| || ||||||||||| |||||||| || |
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG

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|47829276|gb|CK118960.1|CK118960
EST:     GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTGGTGATG                         CTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTG
genomic: GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTGGTGATGgtaattaagc ... cctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTG
EST: gi|86080625|gb|DR376382.1|DR376382
EST:     GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTGGTGATG                         CTGCTGAGTTCCTCCGTAAATCCCYTGAAGGGAAGTATGATGCCATCATTG
genomic: GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTGGTGATGgtaattaagc ... cctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTG
EST: gi|86079304|gb|DR375061.1|DR375061
EST:     GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTAGTGATG                         CTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTG
genomic: GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTGGTGATGgtaattaagc ... cctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTG
EST: gi|47831735|gb|CK121419.1|CK121419
EST:     GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTGGTGATG                         CTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTG
genomic: GTTAGCGGTTGGGTTTGACGATCCTCGTGTTCAACTTCACATTGGTGATGgtaattaagc ... cctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcacaaaacgtagtcaaaaatttgcttgtgttgatatcactttcctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG
                              tgttgat  putative branch site (score: 4)
                                    tatcactttcctct  CT-rich tract
               tcaaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaagcattcttctacttgttctctgttcacaaaacgtagtcaaaaatttgcttgtgttgatatcactttcctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG