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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagatttatgttccacctgtgccttactattctgatttaatttggcttactttcaattgttgaagttgcaccactacacctttgaatttcagtaggat...

Basic information

species Glycine max
transcript GLYMA15G05740.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 8
GCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagatttatgt-tccacctgtgccttactattctgatttaatttggcttactttcaattgttg-aagttgcaccactacacctttgaatttcagtaggat
 |||||| | || ||    |||||  | ||||||||||| || |||||||| || || || ||||| |||| ||| ||||| ||  | |||||||| |||||||||||| | | | | |   |  ||  | | ||    |||||    | |||      ||| ||  |     ||   | ||   |  | ||   |  |   
TCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttctctcttcgctcttcactctccactcattattaataaaacataccacatgttgctgtgaagcatactgatgcagtatacacttgtgggggt--

upper sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 7
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 8
GCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagatttatgttccacctgtgccttactattctgatttaatttggcttactttcaat---tgttgaagttgcaccactacacctttgaatttcagtaggat----
 |||||| |||| |||  ||| ||  | ||||||||||| || |||||||| ||||| || ||||| ||||| || ||||||||| | || ||||| || ||||| | |||  |  |  | | |  |  || ||  || || | |      | ||||     |||||| |       | |     ||||| ||   || |  |    
TCATCATCTGGATGATTCTCAACAGAGCAAAAACTTCACATTCAAATGCCACAGAGATGGAAATGATATATATTCTGTCAACTCTCTGAATTTCCACCCGgtaagctctat-ctatagttatactcttatactcgtatgtattctttgaagccttcagcatatgttga-gcgatgaaaatgattgtttgagttgttgtggatttaag

upper sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 5'ss of exon 7
GCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagatttatgttccacctgtgccttactattctgatttaatttggcttactttcaatt--gttgaagttgcaccactacacctttgaatttcagtaggat---
 || ||| |||| |||   || ||  |||||||||| ||||||||||| ||| ||||||| ||||| ||||||||||| ||||| |||||||| ||||| ||||||||  |||| |         |   | || | ||| | | |   ||  ||  |  |  | |    |||    |  |||   || || |  |||  |     
ACACCATCTGGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGTCATCGAGAGGGAAATGAGATATACTCAGTTAACTCATTAAACTTTCATCCAgtaagattc-tgtttccttcaaatttcctttttgtcattcactgtt-tttgtttgaaggtaggctctcattgt-ttatgacaatcttaaaat--agtttgtctct

upper sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 5'ss of exon 8
GCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagatt-tatgttccacctgt----gccttactattctgatttaatttggcttactttcaattgttgaagttgcaccactacacctttgaatttcagtaggat
 |||||| | || |||   || ||  |||||||||| |||||||||||||| || || |||||||| ||||||||||| |||||| |||||||||||||||||||||| ||  || | | ||     |   || |  |   || ||  |  |   |  | || | ||||    |  |     |     || | | |  |      
ACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATATACTCAGTGAACTCTCTAAACTTCCATCCTgtaagattctacattgcccttgcaatagttctagttattgaatatatctctgtgcatgtgca-tggttgcctgtatattgggagcttgtttattctttgct----

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|8670273|gb|BE191380.1|BE191380
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|18848529|gb|BM567714.1|BM567714
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|24205294|gb|BU964547.1|BU964547
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|16106332|gb|BI894072.1|BI894072
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|21887065|gb|BQ740278.1|BQ740278
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|254327975|gb|GR834940.1|GR834940
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|254327974|gb|GR834939.1|GR834939
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|21887213|gb|BQ740426.1|BQ740426
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|8670281|gb|BE191388.1|BE191388
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|15200978|gb|BI424629.1|BI424629
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|13311248|gb|BG404881.1|BG404881
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
EST: gi|15000181|gb|BI320995.1|BI320995
EST:     ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCT                         GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG
genomic: ATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagattta ... tgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATATACTCAGTCAACTCTTTAAACTTCCATCCTgtaagatttatgttccacctgtgccttactattctgatttaatttggcttactttcaattgttgaagttgcaccactacacctttgaatttcagtaggat

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG