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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttccattcactttttatgcttcagtgaaaatagacatacccttataagattggtttaagcttcaagtttatgattctttctgtatccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G22890.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 4
--gtttccattcactttttatgcttcagtgaaaatagacatacccttataagattggtttaagcttcaagtttatgattctttctgtatccatgt---agATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAG
   |   || | |  ||      | || |   ||| |   ||       |  ||     |     |    ||  | | |  |    || |  | |   |||  || || || || ||||||   ||||||||||| |||||||| ||||||||||||
tattggtcactgaaattagggaatacaattggaattgctttagtagctgagtatctccctccttcttgtattatttactgatctcataactgttttccagAAAGAAGGGAGTGAAATTGTGGCTGAGGGTCCAAGGTGCAGTCTTCGTAGTAAAAAG

upper sequence: AT4G22890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 3'ss of exon 4
---------gtttcca--ttcacttttt---atgcttcagtgaaaatagacatacccttataagattggtttaagcttcaagtttatgattctttctgtatccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAG
         | || ||  ||   |||||    || ||        ||| |  | |   ||| |   || |||   ||||   |  || ||| | | | | |      ||||||| || || || |||||    |||||||||||||||||||| ||||||||||||
gttaatttagctttcaagtttgttttttcctgtgtttggccatccatataattgctgctattattatgcttt---cttcttatccataattttctttttct------agATTGAAGGAAGTGAAATTGTAGTTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG
















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|125204018|gb|EL218972.1|EL218972
EST:     ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGT
genomic: ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGT
EST: gi|125320430|gb|EL334515.1|EL334515
EST:     CTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAAG
genomic: CTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTA-G
EST: gi|125324433|gb|EL338513.1|EL338513
EST:     CAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
genomic: CAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
EST: gi|116431831|gb|EG474423.1|EG474423
EST:     ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
genomic: ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
EST: gi|86028473|gb|DR324226.1|DR324226
EST:     ATCCAATCTTGAATGATGAAGAATATGATAAGCTCANACTCAAACTAAAG                         ATTGATGGTAGCGACA
genomic: ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACA
EST: gi|124939283|gb|EL015837.1|EL015837
EST:     TCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGGGGGTCCAAGATGCAGTCTCCGTAGT
genomic: TCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
EST: gi|116431832|gb|EG474424.1|EG474424
EST:     ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
genomic: ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
EST: gi|124866639|gb|EH951076.1|EH951076
EST:     TCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTC
genomic: TCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTC
EST: gi|124921247|gb|EH994882.1|EH994882
EST:     AATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGA
genomic: AATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGA
EST: gi|125155694|gb|EL185677.1|EL185677
EST:     AATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCC-TAGT
genomic: AATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
EST: gi|125207815|gb|EL222769.1|EL222769
EST:     GATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
genomic: GATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
EST: gi|164006220|gb|ES124350.1|ES124350
EST:     CAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTC
genomic: CAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTC
EST: gi|116424112|gb|EG466704.1|EG466704
EST:     ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAACCTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
genomic: ATCCAATCTTGAATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
EST: gi|125012342|gb|EL084611.1|EL084611
EST:     AATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAG                         ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT
genomic: AATGATGAAGAATATGATAAGCTCAAACTCAAACTAAAGgtttccattc ... atccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttataagattggtttaagcttcaagtttatgattctttctgtatccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAG
                                   ttctttctgtatcc  CT-rich tract
                            tttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttccattcactttttatgcttcagtgaaaatagacatacccttataagattggtttaagcttcaagtttatgattctttctgtatccatgtagATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAG

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