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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttgacagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcag

Basic information

species Arabidopsis thaliana
transcript AT3G59350.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G59350.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G001668_T01 (Zea mays), 5'ss of exon 7
GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttgacagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcag
|||||||||||| ||||||||||||| |||||||||||||| ||||| |   | ||||||||||||||||| || |  || || |||||  |   || | | ||   | | |    ||  | |    ||      || |   ||   |   | | |  | |  |||    |||| | |||||       
GCTACTCCAAGGTTAAGTGAAGACAAGGTGAAGCAATGTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcgacattttacccttc--atactcgtctccgtgaatgatgtttttacatt---aatttggccatcttttattgatgtaatccctt-tccttgcag-----

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G071877_T01 (Zea mays), 5'ss of exon 7
GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttg---acagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcag
|||||||||||| | ||||||||||| |||||||||||||| ||||| |   | ||||||||||||||||| || |  || || |||||  |   || | |   | |   ||   |   |  || |    |    |   | ||    | |  | |       |  |  |||| |||||  ||  | || |||
GCTACTCCAAGGTTGAGTGAAGACAAGGTGAAGCAATGTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattttaccccctcgtacacgtctctgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttc-ccttggactctccctgcag

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G029530_T01 (Zea mays), 5'ss of exon 7
GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttgacagttta-atctata-acccctgcgaaaccact--ttcaaaacgcta-accat----aaaatactgtttcgccttgtt-cttgcgcttcag----------------------
|| || || ||  | | ||| |||| ||| || |||||||||||||||| | | ||||||||||||||||| || |  ||||| ||||| |  ||||||    ||  | |  ||   |   |   |  |   |       |  | |||   |||| || ||    ||   | |      | |||||  || | ||  |                       
GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctg-gcttcaatccttccataccttgtgtgcgtgcgcttccatgggttggttactgcaatctgctatacgatcaggaaggcagtaagcaactttgttgtttacactaaatggtcctcttctgtctgttgcag

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G44210.1 (Glycine max), 5'ss of exon 8
GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttgacagtttaatctata---acccctgcgaaacc-actttcaaaacgctaaccataaaatactgtttcg-ccttgttcttgcgcttcag-----------------------------
|||||||||||  |||||||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||  ||||| ||||||||   |||   || |      | | |  |  |    | | || ||||   ||| |  |  |   ||  |     |  || || |  ||   ||||  | || |                              
GCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggccatacag

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 8
GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttgacagtttaatctata-acccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcg-ccttgttcttgcgcttcag-----------------------------
|||||||||||  |||||||||| |||||||| || || ||||| |||||||| ||||||||||| || || ||||  ||||| |||||||    |||   || |      | | |  |  |  | | || ||||  ||| |  |  |   ||  |     |  || || |  ||   | ||  | || |                              
GCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAACTGAAGGGAGAATACCCCCCCAAAGGAGTTGCTAAGgtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcag

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 5'ss of exon 7
GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttgacagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcag
||||||||||| || |||||||||||||| || |||||||| ||||| ||||||||||||||||||||||| ||||  ||||| ||||| |   |||   || | |  |  | |  ||| |  | ||  |  |  ||||  || ||   |||| |  |  ||    |  |  ||| |   | | | |||
GCTACTCCAAGACTGAGTGAAGACAAAGTTAAACAATGTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAGgtct---ctttgcctctctctctctctc-tctctctcacccacacacacactcacagaaaaataactagtagctaactctgtgaattggtgg-gtgatgcag

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|124713101|gb|EH804503.1|EH804503
EST:     GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGC
genomic: GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGC
EST: gi|124902181|gb|EH976261.1|EH976261
EST:     AAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTT
genomic: AAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTT
EST: gi|124923147|gb|EL001368.1|EL001368
EST:     CCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA
genomic: CCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA
EST: gi|86079614|gb|DR375371.1|DR375371
EST:     GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA
genomic: GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagcttcatctttttgacagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG