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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcatctttcttaagccaatccctagattctattttttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG

Basic information

species Arabidopsis thaliana
transcript AT1G76030.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 10
----gtaaaatcatc-tttcttaagccaatccctagattctattt--tttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG
    ||   ||| |      ||| |  | | ||||   | |  ||  ||||   | | | ||   |  | ||   | ||||  | |  ||   | | ||||||| || ||||||||||| |||||||| || |||||||| ||||| |||||||| || || ||||| || || |||||||||
ttgcgttggatctttaccatttatgttattacctaatgtgtgctttgtttagtcttaaacaataaatatgtttaacattgtgctgtttcatcctaaacagATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
--gtaaaat-catctttcttaagccaatccctagattctattttttatc---ttgagaaaactcaattcttact--cgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG
   |||||  || || || |  |         |||    | || ||  |   || |   || |  |   |  ||    ||||  | | ||   |  | |||||||||| || ||||||||||| |||||||| ||||||||||| || |||||||| || |||||||| || || |||||||||
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatct-actcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G094497_T03 (Zea mays), 3'ss of exon 1
-------gtaaaatcatctttcttaagccaatccctagattctattttttatct--tgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG
        |    ||||  ||  |   |||     |  ||| | ||    || |  |   |  |  | ||   || |  ||||  | | ||   |  | |||||||||| || |||||||| || |||||||| ||||||||||| || |||||||| || |||||||| || || |||||||||
tagcatgttggtctcatgatttatttaccatctatttcattttgttgggcatttaatactagtataccatgtctaat-attgtaatct-acccctaaaacagATATCACACACCCAACTCCTGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 10
gtaaaatcatctttcttaagccaa-----------tccctagattctattttttatcttga-gaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG
||||  | | | || | | |               |||||  |    | || || |  |   ||| |  || | | |        || |||      |  | ||||||| || ||||||||||| |||||||||||||| |||||||| || |||||||| || ||||||||||| |||||| | |||
gtaatgttagcattttcaggatgtctggctattcttccctgcacatcagttcttgtaatagtgaacagacattacctgaaaccaattattttttg--tccaccagATATTACGCATCCAACTCCAGATCTTACTGGTTATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaatcatctttcttaagccaatccctagattctattttttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG
                                               |  || |  ||   || |     |  |    ||||  | |   |||||||||||||||| | ||||||||| ||||||||||||||||| || ||||| ||| | ||  | |||||  ||||  | |||
----------------------------------------------gtacgagatgtctgatcatcgagatcatctactgacttactcg-cagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaatcatctttcttaagccaatccctagattctattttttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG
                                               |  || |  ||   || |     |  |    ||||  | |   |||||||||||||||| | ||| ||||| ||||||||||||||||| || ||||| ||| | ||  | |||||  ||||  | |||
----------------------------------------------gtacgagatgtctgatcatcgagatcatctactgacttactcg-cagATATCACTCATCCGATTCCTGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG

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|116457675|gb|EG500267.1|EG500267
EST:     AAGAAAAGGTTCCATCACCCAAATTCCAATCCTCACTATGCCCAATGACG                         ATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGA
genomic: AAGAAAAGGTTCCATCACCCAAATTCCAATCCTCACTATGCCCAATGACGgtaaaatcat ... aattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGA
EST: gi|124809541|gb|EH895097.1|EH895097
EST:     TCCAATCCTCACTATGCCCAATGACG                         ATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACT
genomic: TCCAATCCTCACTATGCCCAATGACGgtaaaatcat ... aattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACT
EST: gi|125212802|gb|EL227756.1|EL227756
EST:     AAGAAAAGGTTCCATCACCCAAATTCCAATCCTCACTATGCCCAATGACG                         ATATCACTCATCCAACTCCGGA
genomic: AAGAAAAGGTTCCATCACCCAAATTCCAATCCTCACTATGCCCAATGACGgtaaaatcat ... aattgatcagATATCACTCATCCAACTCCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG
                    aattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcatctttcttaagccaatccctagattctattttttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG