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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcgattttgtgcag

Basic information

species Arabidopsis thaliana
transcript AT4G26430.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 5'ss of exon 5
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaag------ctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaatttt--aggttgattcc--tcgat---tttgtgcag
|| || || || || || |||||||||||||||||||| ||||| || ||||||||||| ||||| || |||||||| ||| ||        |||| |||| || || | |  || |   ||   | |  |   ||  |  || |  |||   |   |||| |     |||   |||| ||||
ACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAATgtgagggttcttcttatcatcagtttatgtcttacagatattgagttgtactacccaa-tatattgtttttggaaaaatgatactgacagatatatttgagcag

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagc--tttattatca-------cttcatatttatcata---atctgttctttctttttcatctgcatggaattttaggttgattcctcgattttgtgcag-------------------------------------------
|| || || ||||| || |||||||| || |||||||| ||||| || ||||||||||| || ||||| || |||||||||||||  | || | | |         ||| |   |   ||    || ||   |   ||  |    || | |  || |      ||      ||| |  |  |                                           
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G080652_T01 (Zea mays), 5'ss of exon 5
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagctttattatc-----acttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcg-attttgtgcag-------------------------------------------
|| || || ||||| || |||||||| || |||||||| ||||| || || |||||||| |||||||| || ||||||||||||  |||| ||      || ||  ||    ||      |   | ||||     |     ||   | | |   | |||  ||  | | | ||  |                                           
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcatactgtctgaggtatatttctggacagaattgtactaatcgatgatttcgtgcag

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 5
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcgattt-tgtgcag---------
|| |||||||| ||| ||||||| |||||||||||||| |||||||||||||||||||| || |||||||| || || ||||||  || || |    || | |||  ||| || | ||  || | ||||||             ||||   | |  | ||||| ||| | |         
ACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtaagtgtttttctagactcttctttg-cattatatctttattatctttcattaagcctttggagtaggggaagtgtttgatttctgttctgattgtcagg

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA06G47850.1 (Glycine max), 5'ss of exon 5
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagctttattatcacttcatattt--atcataatctgttctt---tctttttcatctgcatggaattttaggttgattcctcgattttgtgcag----
|| |||||||| ||| | ||||| |||||||||||||| |||||||||||||||||||| || |||||||| || || ||| ||  || || |    || | |||  || || |||| |  ||    ||||    |  |    |  ||||   ||   | ||   | ||  | |     
ACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtgagtgtttttctagactcttctttgcattattatctttcattaagcctttggagtgggggaagtttttttatttctgttcttattgttaggtaattat

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcga----ttttgtgcag---------------------------------------------------------------------------
|| || ||||| ||||| || || |||||||||||||| |||||||| |||||||||||||| || ||||| ||||| |||||||  |  | ||       |||| |  |  | | |  |  | ||||    ||||   |||| ||   |  |||  |      |||| | |                                                                             
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttt----tgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag

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|116443196|gb|EG485788.1|EG485788
EST:     TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGTA
genomic: TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA
EST: gi|86080018|gb|DR375775.1|DR375775
EST:     TCATG-TGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA
genomic: TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA
EST: gi|164060170|gb|ES187667.1|ES187667
EST:     TTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAA
genomic: TTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAA
EST: gi|116443197|gb|EG485789.1|EG485789
EST:     TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGTA
genomic: TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcgattttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC