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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgataggtttctctgcactgtacttattaaagcttctgattgtggatttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G02760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgataggtttctctgcactgtacttattaaagcttctgattgtggatttgcag-------
||||||||||||||||| |||||  ||| ||||| || || || || ||||| || || || || ||||| || ||| ||||||||||||| ||||| ||||| |    |  ||    |            |   ||||  ||| ||    || |   || ||   |  |  | ||  | ||  | |           
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgta-tgatgcagaatccccccgcccccttttccccacttcttagtttgaattgta--atatttgacatcgtctttggatatgcttatttcttttacag

upper sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 5'ss of exon 1
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgataggtttctctgcactgtacttattaaagc----------ttctgattgtggatttgcag------------------------
|||||||||||||||||||| | |||||||| |||||||| || || ||||| ||||| || |||||||| |||||| | ||||||||||| || || ||||| ||         |  |                | | | |   |  ||   || | |  |||| ||             |||| ||| ||| |||   |                        
TGATGAGGGATTTCAAGAGGCTCCAGCAAGATCCACCTGCTGGCATCAGTGGGGCTCCTCAGGACAACAACATCATGCTATGGAATGCTGTCATTTTTGGgtatttctttctttctctctttctttctttttttgattggttttttgccttaccattttgtttatcaacttgttttgataattctaattctgggtttttggtgttttttcttgtttgatttgtag

upper sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgatag-gtttctctgcac-tgtacttattaaagcttctgattgtggatttgcag---------
||||| | || |||||| |  ||||||| || || || || || || || || || || || |||||||| |||||||||||||||||||| |||||||||||    ||||       | |            || ||  || | ||   | || |   | | ||  |   ||       | || ||  || |         
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaactcctccc-cgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatg-gcggtgtcggttt

upper sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaa-------ctaaagtaacaaaaaaaaaaaacgatacttgataggtttctc--tgcactgtacttattaaa---gcttctgattgtggatttgcag
||||| | || |||||| | ||||| || || || || || || || || || ||||| || ||||||||||||||| ||||||||||||| ||||||||||||   |        ||    |            ||  |   |  |    | | |    | | | |  | |   |      | || || ||| | |||    
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcctccctggtttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt---

upper sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgataggtttctctgcactgtacttattaaagcttctgattgtggatttgcag
||||| | ||||||||| |  | ||||| || || || ||||| || || || |||||||| ||||||||||||||||||||||||||||| || ||||||| | |   ||   | |||       |       |   || | ||||  |    || |                                 
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagtt--ctcgcgaaacctttcttagggtttttgaatg-tcggttctttcttacag---------------------------------

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|125069497|gb|EL135252.1|EL135252
EST:     CAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: CAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|301503183|gb|HO208723.1|HO208723
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|116431365|gb|EG473957.1|EG473957
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|124745520|gb|EH836332.1|EH836332
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|125111740|gb|EL163097.1|EL163097
EST:     TGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: TGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|124769329|gb|EH859459.1|EH859459
EST:     AGACAACAATATCATGTTGTGGAANGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: AGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|124994773|gb|EL067042.1|EL067042
EST:     CAACAATATCATGTTGTGGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAGGTACTTT
genomic: CAACAATATCATGTTGT-GGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAGGTACTTT
EST: gi|125024080|gb|EL096349.1|EL096349
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGA
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGA
EST: gi|116428641|gb|EG471233.1|EG471233
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|124744803|gb|EH835965.1|EH835965
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAGGTA
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAGGTA
EST: gi|124762989|gb|EH853119.1|EH853119
EST:     TATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGAATGGAG
genomic: TATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGA-TGGAG
EST: gi|116454996|gb|EG497588.1|EG497588
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|125013440|gb|EL085709.1|EL085709
EST:     AATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: AATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG
EST: gi|301502531|gb|HO208071.1|HO208071
EST:     GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGG                         GCCTGATGATACCCCTTGGGATGGAG
genomic: GGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaac ... ggatttgcagGCCTGATGATACCCCTTGGGATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgataggtttctctgcactgtacttattaaagcttctgattgtggatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT