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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactcttcatatgattcatatactagtgattgattaatgatttttgttattgataaatgtcttgtgtgtgttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G72370.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 2
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactcttcatatgattcata---tactagtgatt-gattaatgatttttgt-tattgataaa--tgtcttgtgtg-tgt-tgcag
|||||| || |||||||||||||| || ||||| ||| ||||||| || |||||||| ||| | ||  | || || |||||||| || ||||| || |||||||  | |   |||| || ||    |  | || ||| |||     | ||  ||  | |   ||   || ||  |||  ||| | |||
TGCTGGTAGGCACACTCCTGGTACATTTACCAACCAGCTGCAGACCTCATTCAGTGAGCCACGCCTTCTTATCCTGACTGACCCCAGGACTGATCATCAGgtaagatttcagtatgtttgattgtttcttggtaatttgatctgccaattgagtgcactctcaagcctgcctgttgtaatgtgtacag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G145308_T01 (Zea mays), 5'ss of exon 2
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaa-------ctcttcatatgattc-------atatac-tagtgattgattaatgatttttgttattga--taaatgtcttgtgtg--tgtt-gcag
 ||||| || ||||| ||||||||||||||||||||| | ||||| ||||||||||| ||  | ||| | || |||||||||||||| |||||||||||||| ||        |  |   |   |||       |||||   | ||| ||  |  ||  || || |  |||  |||  ||  || ||   |||| ||||
CGCTGGGAGGCACACCCCTGGTACCTTCACCAATCAGCTCCAGACCTCCTTCAGTGAGCCTCGCCTGCTCATCCTTACTGACCCAAGGACTGACCACCAGgtgaagagaagttttgtttcaaagttcttaagaaatatatgcattgagtgggtgctgcattgtgatggtgaactaatagttatgcgtaattgtttgcag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G099657_T01 (Zea mays), 5'ss of exon 2
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactcttcatatgattcata-tactagtgattgattaatgatttttgttat-tgataaatgtcttgt-gtgtgttgcag-------
 ||||| || ||||| ||||||||||||||||||||| | ||||| || ||||| || ||  | ||| | || |||||||||||||| |||||||| ||||| ||       | || | || | | ||   ||   ||| |||| |  ||   | ||||  |    |||| ||| ||  | |       
CGCTGGGAGGCACACCCCTGGTACCTTCACCAATCAGCTCCAGACCTCTTTCAGCGAGCCTCGCCTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgaagggaatttctgttccaaagttcttacgaaatatttatgaatgctgcagtgtgatggactaattgtagtgcgtaactgtttgcag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaact---cttca----tatgattcatatac---tagtgattgattaatgatttttgttattga--taaatgtcttgtgtgtg-----ttgcag
 ||||| || ||||| |||||||||||||| || ||| | ||||| |||||||| || ||  ||||| | || ||||| |||||||| |||||||| ||||| |||     ||||     |   |||| | |    |||||| ||     ||   | || |  |||  ||| |||  ||   |||     ||||||
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G092719_T01 (Zea mays), 5'ss of exon 2
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaa-actcttcatatgattcatatact--agtgattgattaatgatttttgttattgataaatgtcttgtgtgtgttgcag--------------
 ||||| || ||||| |||||||| ||||| |||||| | ||||| |||||||| || ||  | ||| | || |||||||||||||| |||||||| ||||| | | |  |   |   |  |  | ||  |||  ||  | | ||     ||   |       ||   |   |||  ||| |              
CGCTGGGAGGCACACCCCTGGTACATTCACTAATCAGCTCCAGACCTCCTTCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatagtttcagtttcaaagttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaattgttatgctggtaatcgtttgcag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G159237_T03 (Zea mays), 5'ss of exon 1
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactcttcatatgattcatatactagt-gattgattaatgatttttgtt-attgataaatgtcttgtgtgtgttgcag---------------
|||||| || |||||||||||||| |||||||| ||| |||| || ||||||||||| ||| | ||  | || || |||||||| || ||||| || ||||||||   |  || || |  |   |  | | ||  |   ||     |||| | ||| | |    | |    | |  |  |                
TGCTGGCAGGCACACTCCTGGTACATTCACCAACCAGTTGCAAACCTCCTTCAGTGAGCCACGCCTTCTTATCCTGACTGACCCGAGGACTGATCATCAGgtaaaacttatatctgttgaaagaaaaactagagcgtgcaactcggtttgctgattcagaggactttaaaatcttctttatccaaactttgtacag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G04890.1 (Glycine max), 5'ss of exon 2
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaac------tcttcatatg-attcatat-actagtgattgattaat--gatttttgttattgataaatgtcttgtgtgt-gttgcag--------------------------------------------------------------------------------
||||||||| ||||||||||||||||||||||||||| | || || |||||||| || ||  | ||  | |||||||| || |||||||| || |||||||| |        | |||||||| | | |||| |  |   |  |||  ||  |||| | || |    |   |   |||  ||| | || ||                                                                                
TGCTGGAAGGCACACTCCTGGTACCTTCACCAATCAGCTTCAAACTTCCTTCAGCGAGCCTCGTCTCCTTATTCTTACCGATCCAAGAACAGATCACCAGgttagtaccctattttcatatgcagttatatgaagaaaaaaagatacatttgattctagtcacatgtggtttgattgattgttgatgtagtttatggtgtgattgtttgtttagggttgttgtattgcccgtgttgtgttgttaatgtatgtttgttggtttgtgtgcag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G01460.1 (Glycine max), 5'ss of exon 2
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactcttca-tatgattcatatactagtgattgatt--aatgatttttgtt---attgataaatgtcttg-tgtgtgttgcag------------------------------------------------------------------------
||||||||| |||||||| |||||||||||||||||| | ||||| || |||||||| ||  | ||  | || || ||||| |||||||| || ||||||||  |  |   | |  | |||| ||  || |  ||||||  | | | || || |   ||||||   || | || | | ||||                                                                            
TGCTGGAAGGCACACTCCCGGTACCTTCACCAATCAGCTTCAGACTTCGTTCAGTGAGCCTCGTCTCCTTATCCTCACTGATCCAAGAACAGATCACCAGgtggatacccaaatcagcttcaaatgata-tatttgattttagttacttgtgctttgattgattgttgacatgatttatgttatgtatgttgtttgcggttgttgtggtgttgactgtgttgtgttgttaatgtgtgtgtttgttcgtttgtgtgcag

upper sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 5'ss of exon 2
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactcttcatatg-attcatata---ctagtgattgattaatgatttttg-ttattgataaatgtcttg--tgtgtgttgcag--------------
||||||||| ||||| || ||||| |||||||||||| | |||||||| |||||||| ||  | ||  | || || || |||||||||||||| ||||||||||     | | |   ||   ||||      ||  ||  ||   | |||  | ||   |  |  ||  | |  |   | ||  ||              
TGCTGGAAGGCACACACCAGGTACATTCACCAATCAGCTCCAGACATCTTTCAGTGAGCCCCGTCTTCTCATCCTCACAGACCCAAGAACTGATCACCAGgtaagtgaataacacacatctttataaattctgtttttagtttgggttttagggttcaaggaaggtgcgtagactactttttctagccaaccagggaaat

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|164118810|gb|ES037484.1|ES037484
EST:     GAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: GAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|116467170|gb|EG509762.1|EG509762
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|164230555|gb|ES068878.1|ES068878
EST:     ACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGG-AACATTCCAATCATTGCTTTCTGTGAC
genomic: ACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|116423188|gb|EG465780.1|EG465780
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|164028003|gb|ES181151.1|ES181151
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACA
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACA
EST: gi|125149326|gb|EL182545.1|EL182545
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGG
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGG
EST: gi|301501781|gb|HO207321.1|HO207321
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|164199635|gb|ES181304.1|ES181304
EST:     GACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: GACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|125192039|gb|EL206993.1|EL206993
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCT
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCT
EST: gi|116470236|gb|EG512828.1|EG512828
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|124917032|gb|EH990906.1|EH990906
EST:     AACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: AACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|125275690|gb|EL289775.1|EL289775
EST:     CTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: CTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|124999382|gb|EL071651.1|EL071651
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTCTGGGAAACATTCCAATCATTGCTTTCT
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCT
EST: gi|164216655|gb|ES088221.1|ES088221
EST:     CAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: CAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|164128782|gb|EL975371.1|EL975371
EST:     GAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: GAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|164072395|gb|ES080933.1|ES080933
EST:     AGTGAACCAAGGCTGTTGTATTTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTC
genomic: AGTGAACCAAGGCTGTTG-A-TTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTC
EST: gi|116470237|gb|EG512829.1|EG512829
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|47830956|gb|CK120640.1|CK120640
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGAC
EST: gi|164172062|gb|ES134641.1|ES134641
EST:     TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAG                         CCTATCAAGGAAGGTGCTTTGGG
genomic: TCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactctt ... tgtgttgcagCCTATCAAGGAAGGTGCTTTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaactcttcatatgattcatatactagtgattgattaatgatttttgttattgataaatgtcttgtgtgtgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC