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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag

Basic information

species Arabidopsis thaliana
transcript AT4G10610.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgc-ttagtttcacttttcaacag
 | || ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||        ||  |||    | ||   || |       ||| ||  |   | ||||| ||   || || || | | || ||   | |||
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgta-----tgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttct---ttggcatttgatgcatttgata-cag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G457231_T01 (Zea mays), 5'ss of exon 8
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtg----------actctcactcgaataaattggtttcc--tttgccaaa---ctattctgaaactta-atgttgct-aactttgcttagtttcacttttcaa--cag--------------------------------------------------------------------
 |||| ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||           ||||   ||   |  | | ||| | |  | || ||     ||||| | | ||    | ||  || ||   |   ||   | | | ||  |  ||                                                                     
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAGgtattcattctgtcatgattctattttaatacacgtaggtcactcaagcatatctaaacttattctttgagtcaatatgtggtgaggttggtcgttctttactccaaacacaatctcccttctgtacaactaaaagtttgcag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G069102_T01 (Zea mays), 5'ss of exon 6
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaat-tggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||   |   ||    |   ||     | ||  |    |   ||||||  | |   | |   | | |   |  ||                
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgt--ttggtacctacactcatgctactaccactatgtattcattctgtca-tggttctgttttaatacacgcag----------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G454261_T01 (Zea mays), 5'ss of exon 2
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaat-tggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||   |   ||  | ||  ||     | ||  |    |  |||| ||  | |   | |   | | |   | |||                
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgt--ttggtacctgcattcatgctactaccactagttatttattgtgtca-tggttctgttttaatacacgtag----------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G123866_T01 (Zea mays), 5'ss of exon 11
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaat-tggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||   |   ||  | |   ||     | ||  |    |   ||||||  | |   | |   | | |   |  ||                
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgt--ttggtacctgcactcatgctactaccactaggtattcattctgtca-tggttctgttttaatacacgcag----------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G166091_T01 (Zea mays), 5'ss of exon 8
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaat-tggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||   |   ||  |||   ||     | ||  |    |   ||||||  | | | | |   | | |   |  ||                
TCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAGgt--ttggtacctgaactcatgctactaccactaggtattcattctgtca-tgattctgttttaatacacgcag----------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G310936_T01 (Zea mays), 5'ss of exon 1
---------------------------------ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaat-tggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
                                 ||||| ||||| ||||| ||||||||||| ||||||||| |||| |||||||||||||||||   |   ||  | ||  ||     | ||| |    |   ||||||  | |   | |   | | |   |  ||                
ATGACATATATACTTATTTTCTGTGCTCTGCAGACTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACCGCACAAACATTGACAAGAAGgt--ttggtacctgcattcatgctactacctgtagttattcattctgtca-tggttctgttttaatacacgcag----------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G014573_T01 (Zea mays), 5'ss of exon 4
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| || ||||||||||| |||||||||||||||||   |   ||  | |   ||  | | |       |   |||||    |  | ||| | |||  ||     |                 
CCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAGgt--ttggtacctgcactcat--gctactaccattagg-tattc-attatgtcatggttctattttaatacacgcag------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G044246_T01 (Zea mays), 5'ss of exon 2
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtg----------actctcactcgaataaattggtttcc--tttgccaaa---ctattctgaaactta-atgttgct-aactttgcttagtttcacttttcaacag--------------------------------------------------------
 |||| ||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||||||           ||||   ||   |  | | ||| | |  | |  ||     || || | | ||  | | ||  || ||       ||   | | | ||  |                                                           
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAGgtattcattctatcatggttctgttttaatacacacaggtcactcaagcagatctaaagttattctttgagtccatatgtggtgaggttggtcgttctttactgcaaacacaatctcccttctgtatag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G376619_T01 (Zea mays), 5'ss of exon 7
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaat-tggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| |||||||||| ||| |||||||||||||||||   |   ||  | |   ||     | || ||    |   ||||||  | |   | |   | | |   |  ||                
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTACACAAACATTGACAAGAAGgt--ttggtacctgcactcatgctactaccattaggtattcattctgtca-tggttctgttttaatacacgcag----------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G044246_T02 (Zea mays), 5'ss of exon 6
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||||||   |   ||  | |   ||  | | |     | |   |||||    | |  ||  || |   | || ||   | |||          
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGgt--ttggtacctgcactcat--gctactaccactagg-tattc----attctatcatggt---tctgttttaatacacacag------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G349794_T01 (Zea mays), 5'ss of exon 7
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| ||||| ||||||||||| |||||||||||||| ||||||||||||| |||   |   ||  | |   ||  | | |       |   |||||       | ||||   |   | || ||   | |||          
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGATGgt--ttggtacctgcactcat--gctactaccattagg-tattca------ttatgtca-tggttctgttttaatacacgcag------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G398795_T01 (Zea mays), 5'ss of exon 8
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 || | ||||| | ||| ||||||||||| |||||||||||||| |||||||||||||||||   |   ||  | |   ||  | | |     | |   |||||       | ||||   |   |||| ||   | ||           
TCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgt--ttggtacctgcactcat--gctactaccactagg-tattca------ttatgtca-tggttttgttttaatacatgcag------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G324221_T03 (Zea mays), 5'ss of exon 7
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaat-tggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| |||||  |||| |||||||| || |||||||||||||| |||||||||||||||||   |   ||    |   ||     | ||  |    |   ||||||  | |   | |   | | |   |  ||                
TCTGACGATGAATGTGAAATGTGTGCTAGGACTATCTACTGCACAAACATTGACAAGAAGgt--ttggtacctacactcatgctactaccactaggtattcattctgtca-tggttctgttttaatacacgcag----------------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G173428_T02 (Zea mays), 5'ss of exon 5
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| || || |||||||| || ||||| |||||||| |||||||||||||||||    |  ||    |   ||    | ||  |        ||||||    | | |||| ||   ||    ||  | |||||     |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt--tccctacctacactcatgctataccactaggtgttcattctg----tcattgtt-ctgttttaatata--tgcacttgctg-cag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G036634_T01 (Zea mays), 5'ss of exon 15
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| || || |||||||| || ||||| |||||||| |||||||||||||||||    |  ||     || | |  |    |    | |  | |||   |   |    ||| |   |||   ||  | ||||| |   |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt--tccctacc----tacactcatgctataccactaggtgttc---attctgtcattgttttgttttaatatatgcacttgttg-cag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G161649_T01 (Zea mays), 5'ss of exon 4
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| || || |||||||| || ||||| |||||||| |||||||||||||||||    |  ||    |   ||    | ||  |  |     ||||||    | | |||| ||   ||    ||  | |||||     |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt--tccctacctacactcatgctataccactagctgttcattctg----tcattgtt-ctgttttaatata--tgcacttgctg-cag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G132286_T01 (Zea mays), 5'ss of exon 5
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
 |||| ||||| || || |||||||| || ||||| |||||||| |||||||||||||||||    |  ||    |   ||    | ||  |        ||||||    | | |||| ||   ||    ||  | |||||   | |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt--tccctacctacactcatgctataccactaggtgttcattctg----tcattgtt-ctgttttaatata--tgcacttgcta-cag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G175541_T02 (Zea mays), 5'ss of exon 5
------------------------------------ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCAC----TAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag
                                     || | ||||| | ||| ||||||||||| ||||||||||||||    ||||||||||||||||||   |   ||  | |   ||  | | |     | |   |||||    | |   |||   |   |||| ||   | |||          
CTCTAAGAAAGTTGGTCGATTTTCTGTGCTCTACAGTCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAATTAACATTGACAAGAAGgt--ttggtacctgcactcat--gctactaccactagg-tattc----attc--tgtca-tggttttgttttaatacacgcag------

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G175541_T01 (Zea mays), 5'ss of exon 2
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCAC----TAACATTGACAAGAAGgtg----------actctcactcgaataaattggtttcc--tttgccaaa---ctattctgaaactta-atgttgct-aactttgcttagtttcacttttcaacag--------------------------------------------------------
 || | ||||| | ||| ||||||||||| ||||||||||||||    ||||||||||||||||||           ||||   ||   |  | | ||| | |  | || ||      | || | | ||    | ||  || ||       ||   | | | ||  |                                                           
TCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAATTAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAGgtattcattctgtcatggttttgttttaatacacgcaggtcactcaagcagatctaaagttattctttgagtccatatgtggtgaggttggtcgttctttactccaaacacaatctcccttctgtatag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 5'ss of exon 7
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcac--tcgaataaattggtt-tcctttgccaaactattctgaaac--ttaatgttgctaactt--tgcttagtttcacttttcaacag--
| ||||||||| || ||||||||||||||||| || ||||| || || ||||| ||||||||   | | |   |    || ||||  | | ||  |    |  | |  |||||  ||  | ||   || |   || |   |||   | || ||     
AATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAGgtactttttatgtttctttatattgaatgtgctccggtgtaggactaggaaacactttttcttttcaaatcaatgttgtatttgtttgtttaatgcag

upper sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 5'ss of exon 6
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaa---ttggtttcctttgccaa--actattctgaaacttaatgttgctaacttt-----gcttagtttcacttttcaacag-
 |||||||||||||||| ||||||||| | || |||||||| || || ||||||||||||||||     | |  |||| |   | | | | || |||  |  |  |     |  | |  |  |||   ||||     | | |||| | ||| ||      
TCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAGgtgaagtggagtgaaatagaatttcgttgttctatgctgacgatgagatccatccgttttactgcctgcttttttgcgataagttgctcttctctttgtg

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|116466690|gb|EG509282.1|EG509282
EST:     AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG                         CTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTGT
genomic: AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctca ... ttttcaacagCTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTGT
EST: gi|124988697|gb|EL061065.1|EL061065
EST:     CTATCTACTGCACTAACATTGACAAGAAG                         CTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTGTGGCGAGGTG
genomic: CTATCTACTGCACTAACATTGACAAGAAGgtgactctca ... ttttcaacagCTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTGTGGCGAGGTG
EST: gi|125002624|gb|EL074893.1|EL074893
EST:     AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG                         CTCACTCAAACCGACATTAAACTCTTCTTTGAGT
genomic: AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctca ... ttttcaacagCTCACTCAAACCGACATTAAACTCTTCTTTGAGT
EST: gi|116466689|gb|EG509281.1|EG509281
EST:     AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG                         CTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTGT
genomic: AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctca ... ttttcaacagCTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTGT
EST: gi|116412046|gb|EG454638.1|EG454638
EST:     AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG                         CTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTG
genomic: AGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctca ... ttttcaacagCTCACTCAAACCGACATTAAACTCTTCTTTGAGTCTGTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgcttagtttcacttttcaacag

- - - - - - -  GAGATG
- - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG