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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA

Basic information

species Arabidopsis thaliana
transcript AT1G19920.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 2
gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtg-tagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
                      |   || |||   |    |   ||||| |      | |   |   | ||  |    | || || ||  ||||| |||||||||| || ||||| ||  |||||||||| || || || || || || |||||||| |||||||||||||| ||||| |||||||| || |
----------------------gtaatcatttgtttatgcagttatttgcta-gttcaaactgtgcaaattactaaattgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA

upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 2
gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
||  | |||||  ||  |   |      |||| ||       | || | || |  | |  | | | |           |||| |||   ||||| ||||||||||||| ||||| ||  |||||||||| || || || ||||| ||||| ||||| |||||||||||||| ||||| || ||||| || |
gtatacatttgtcgtcttaatcttagctgtttacc-------ggatgtattatgcaaattgctgaag----------tttatcatgcacagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTTCCCTCACCAATGCATTATGCTGGTCCAACAGAAGTGCAGTGGCATGCAA

upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
                                                                                                      |||   | |   |       || ||||     |  | |||   | | ||    |   ||| |  |  ||||||| |  |   ||||| |||||||||||||||||||| ||  ||||||| || ||  | || ||||| ||||| ||||| |||||||||||||||||||| || ||||| || |
gtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcattcaatttcagtaatctactcattttgtaattgcacaatccatgg-aattttatcctataaagttctttgcttcttct---tagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA

upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G05020.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------------------gtgcatatttgctgttgtttccgagttcgttttcctcataaa-gaatttgttgtaaagagagattatgatttgatttgcttatgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
                                                                                              || |   |  ||    |||   | |    |    |  |||  | |       |  |     ||| | |     ||   |  |  |   ||||| |||||||||||||||||||| ||  ||||||| || ||  | || ||||| ||||| ||||| |||| ||||||||||||||| || ||||| ||||
gtaattcccattgttcttctcaaaaaacaaagactaatcataatgtgcatgtgctacaacaatagatgttaaaaaaatgaccttgaaaagtgattgaactatcactcaaatttagcaatctactcattttgtaattgcacaatccatggaattttattct-accaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATCGTTGCCATATTTCCATCACCTATGCATTATGTTGGTCCAACTGAAGTACAGTGGCATGCCA

upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 2
gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagatt-atgatttgatttgcttatga------------tgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
     |||||     | ||  | ||||  |    ||  |||| | ||  |||| | | |   |  |   ||  |||| |||||              ||   |||| |||||||||||||| ||||| ||  | ||||| |||||  | || || || ||||| ||||| ||||| || ||||||||||| |||||||| ||||
--ttttattttagtcttttgacaagtttatgaaact--taaaaatttaattgtcatgtgttgtccaaagttcaattttcttattcaaattttatttttggacagGTCCTAGAAGATGGAGTCCTTGATCCTGAAACTACCATTGTGGCTATATTCCCATCACCTATGCATTATGCAGGCCCAACTGAAGTACAATGGCATGCCA

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|86034476|gb|DR330229.1|DR330229
EST:     CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAG                         GTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
genomic: CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAGgtgcatattt ... tgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
EST: gi|86034470|gb|DR330223.1|DR330223
EST:     CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAG                         GTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
genomic: CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAGgtgcatattt ... tgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
EST: gi|86034473|gb|DR330226.1|DR330226
EST:     CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAG                         GTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
genomic: CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAGgtgcatattt ... tgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
EST: gi|86034472|gb|DR330225.1|DR330225
EST:     CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAG                         GTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
genomic: CTGATGATGTTCCTCTTGATGTTAGAATGGAACAACATAGCAAGgtgcatattt ... tgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT
EST: gi|125155631|gb|EL185645.1|EL185645
EST:     GATGTTAGAATGGAACAACATAGCAAG                         GTTCTAGAAGATGGNGTTCTTGACCCGAAGACTACTATTGT
genomic: GATGTTAGAATGGAACAACATAGCAAGgtgcatattt ... tgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGT
EST: gi|164230936|gb|ES011766.1|ES011766
EST:     GGAACAACATAGCAAG                         GTTCTAGAAGATGGAGTTCTTGACCCGAAGACCACTATTGTCTCGATCTTT
genomic: GGAACAACATAGCAAGgtgcatattt ... tgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
                               atttgat  putative branch site (score: 5)
                         attatgatttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG