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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctttttacttctgttttttcattcttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT

Basic information

species Arabidopsis thaliana
transcript AT3G13920.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13920.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------gtctttttacttctgttttttcattcttg----agtgtgttctctccgcatgctctagctgctaattgtactgtattgata---------cagACTTGAG---GGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT
                                                               || || ||  ||    ||    ||  |||    ||  |||| |  |    || || |  |  |||| |   | ||||  |          |||||||      |    | | || ||||||||||||||||| || ||| |||| || ||||| || |||||| | || ||||| ||||||||||| |||||    
gtaagattttttatttttattattcggagcaatctggttttattattactgaaattgctgttcgtgttcttgttttgtgttggatatgattgcaacaggatgttattgctatctgttcaattttttaatggccttatatttttttttccctttcagACTTTCATCTGATGGACAGGACTTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAGAATCTTCTCAGGGGAATTTAC---

upper sequence: AT3G13920.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------------gtctttttacttctgttttttcattcttgagtgtgttctctccgcatgctctagctgctaattgtactgtatt-gatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT
                                                                                        |      |      | ||    || |    |   || |        ||  || || ||  || | |  | |  ||     |  ||| ||||| ||    ||||||||||||||||| || ||| |||| || ||||| || |||||| | || || || ||||||||||| |||||    
gtaagattttttgtttttgtttttatctttcttctgagcaatctggttttattattactgaaacgttcttgttttgtgtcgaatatgattgcaacaggatgatgttaatgttatctgttaaattttaattaatggccttatcttcttttttttccctttcagACTTTCATCTGATGGACAGGAC---TTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTAC---

upper sequence: AT3G13920.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 1
------------------------------------gtctttttac----ttctgttttttcattcttgagtgtgt---tctctccgcatgctctagc-tgctaattgtactgtattg-----------------atacagACTT--GAGGGACAAG-ATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT
                                     | ||||||      ||||||||   | | |  | | |     |||  |    ||   |||  |||||||| |  | | |||                 |||||| |||   |  ||     | || ||||||||||| |||||||| ||| |||| || |||||| | |||||| | |||||||| |||||||| || ||||||   
gtaaggaatacactcctcttttttctttccctccctttttttttataatactctgttttgaaaatttcaaatttaaaagtctacctatgtgtaataggatgctaattttcttttcttggttttatgaatcgatgcatacagGCTTTCAACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTAT---

upper sequence: AT3G13920.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 2
----------------------gtctttttacttctgttttttcattct-tgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT
                       | |||      |   ||||  |||   |||| |||||   | || || |        | | || | ||  |      |      |  |    |||||| ||| |  |  | |  || || || || ||||  ||||| | |||||||||||| |||||||||||||||||||| ||    
ccccaaaagcattggatcttaaatttttcgggggcgaattttctatttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC---

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|86034984|gb|DR330737.1|DR330737
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034973|gb|DR330726.1|DR330726
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|116436248|gb|EG478840.1|EG478840
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035139|gb|DR330892.1|DR330892
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034992|gb|DR330745.1|DR330745
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT---A                         -CTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034913|gb|DR330666.1|DR330666
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035064|gb|DR330817.1|DR330817
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034985|gb|DR330738.1|DR330738
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035170|gb|DR330923.1|DR330923
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034997|gb|DR330750.1|DR330750
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035066|gb|DR330819.1|DR330819
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034888|gb|DR330641.1|DR330641
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034967|gb|DR330720.1|DR330720
EST:     GCACACAGTTTGATGCACGTCAGTTTAACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|47829698|gb|CK119382.1|CK119382
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035051|gb|DR330804.1|DR330804
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035092|gb|DR330845.1|DR330845
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034884|gb|DR330637.1|DR330637
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034857|gb|DR330610.1|DR330610
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|116420410|gb|EG463002.1|EG463002
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035131|gb|DR330884.1|DR330884
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATTTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035037|gb|DR330790.1|DR330790
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|116403403|gb|EG445995.1|EG445995
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034886|gb|DR330639.1|DR330639
EST:     GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAA--GT--                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTGTGAgtctttttac ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT
                                 taattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctttttacttctgttttttcattcttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA