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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGCCAACTTCCATGTGTACACTGCATTGTTAAAGCCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaagttaactttgtatgtcatttcggaactctctgactctgatgaataacagtttctttcttcttatttctcatcag

Basic information

species Arabidopsis thaliana
transcript AT4G37930.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 6
TCCTGCCAACTTCCATGTGTACACTGCATTGTTAAAGCCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaagttaactttgt--atgtcatttcggaactctctgactctgatga---------ataacagtttctttcttcttatttctcatcag-----
 ||||||||||||||||| ||||||||  | || || || ||||| |||||||||||  | ||||||||||||||||| ||||||||||| || || ||||| | |     |  ||||  |   || |   |    |||   ||  || | ||          ||||   || ||| ||| || | | || |        
ACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggtctggacttcttcattgcctccttactactagttgtttcagttggcatgcaagcataatgcttccttccttgttgtctttctttgtcctca

upper sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
TCCTGCCAACTTCCATGTGTACACTGCATTGTTAAAGCCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaagttaactttgtatgtcatttcggaactctctgactctgatg--------aataacagtttctttcttct-tatttctcatcag--------
 || |||||||||||||| ||||||||| | || ||||| |||||||| ||||||||  | ||||||||||| ||||| ||||||||||||||||| ||||| | |     |  | |||   ||| |  ||  |    | | | | |||||        ||  |  | |  || ||||| | || |   ||          
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgt-acctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct

upper sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 6
TCCTGCCAACTTCCATGTGTACACTGCATTGTTAAAGCCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgc--cttcaagttaactttgtatgt--catttcggaactctctgactctga---tgaataacagtttctttcttctta---tttctcatcag----------------------------------------------------------------------
 || ||||| || || || ||||| ||  | |||||||| || ||  | || |||||  | ||||||||||||||||||||| | |||||||| |||||||||    | | | | |||| |   |||  ||| |     | ||| | ||| ||   | ||| |   | |    || || |   |  || ||                                                                         
CCCAGCCAATTTTCAGGTCTACACAGCTCTCTTAAAGCCACACGAGCGCATAATGGCCTTAGATCTTCCTCATGGTGGTCATTTGTCTCATGGATATCAGgtgtgattcctaataaactctacctgtaccatcttttgccactc-gcctcagagcgtcaattattatgtaccgctgctaaagatagcttatttatttatgtatagctgatgttttctccacttgccttacatctactggctctgttgtctgacatggtaaacag

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|125041178|gb|EL113447.1|EL113447
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTA
EST: gi|124877772|gb|EH957209.1|EH957209
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTT
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTT
EST: gi|124825626|gb|EH910492.1|EH910492
EST:     TGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: TGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|116444483|gb|EG487075.1|EG487075
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAAT
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAAT
EST: gi|124910875|gb|EH984955.1|EH984955
EST:     ACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAA
genomic: ACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAA
EST: gi|125047679|gb|EL119948.1|EL119948
EST:     CATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: CATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|86042971|gb|DR338726.1|DR338726
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|124957869|gb|EL032658.1|EL032658
EST:     CTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: CTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|125212205|gb|EL227159.1|EL227159
EST:     TCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: TCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|116443767|gb|EG486359.1|EG486359
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|116433176|gb|EG475768.1|EG475768
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAAT
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAAT
EST: gi|116432208|gb|EG474800.1|EG474800
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|125300153|gb|EL314238.1|EL314238
EST:     ATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAG
genomic: ATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAG
EST: gi|125118003|gb|EL166900.1|EL166900
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAG
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAG
EST: gi|164095384|gb|ES200124.1|ES200124
EST:     CATGGCACTTGATCTTCCTCTATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAG
genomic: CATGGCACTTGATCTTCCTC-ATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAG
EST: gi|125214801|gb|EL229101.1|EL229101
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGA
EST: gi|116428932|gb|EG471524.1|EG471524
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCC
EST: gi|86042972|gb|DR338727.1|DR338727
EST:     TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAG                         ACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTT
genomic: TCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaa ... ttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGCCAACTTCCATGTGTACACTGCATTGTTAAAGCCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaagttaactttgtatgtcatttcggaactctctgactctgatgaataacagtttctttcttcttatttctcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG