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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctttttacttctgttttttcattcttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

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

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

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 2
------------------gtgagtctttttacttctgttttttcattct-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|86034973|gb|DR330726.1|DR330726
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034937|gb|DR330690.1|DR330690
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035064|gb|DR330817.1|DR330817
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035170|gb|DR330923.1|DR330923
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035160|gb|DR330913.1|DR330913
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCSTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035037|gb|DR330790.1|DR330790
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|47829698|gb|CK119382.1|CK119382
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034857|gb|DR330610.1|DR330610
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|116403403|gb|EG445995.1|EG445995
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034967|gb|DR330720.1|DR330720
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTAACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035092|gb|DR330845.1|DR330845
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034880|gb|DR330633.1|DR330633
EST:     AAGGCACACAGTTTGNATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCCTATGATGATGTTCATGAGA
genomic: AAGGCACACAGTTTG-ATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACAT-CCTATGATGATGTTCATGAGA
EST: gi|86035139|gb|DR330892.1|DR330892
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|116436248|gb|EG478840.1|EG478840
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034992|gb|DR330745.1|DR330745
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035125|gb|DR330878.1|DR330878
EST:     GAAGGCACACAGTTTGATGCACGTCAGTATGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86035051|gb|DR330804.1|DR330804
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034997|gb|DR330750.1|DR330750
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|116420410|gb|EG463002.1|EG463002
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034913|gb|DR330666.1|DR330666
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034888|gb|DR330641.1|DR330641
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034886|gb|DR330639.1|DR330639
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST: gi|86034984|gb|DR330737.1|DR330737
EST:     GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT                         ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... 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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctttttacttctgttttttcattcttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT

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