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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttactcttcagaaatatttggaacaaaatacttgtagaatgtgaagtttacttctcccattatcaccattgtggtgtt...

Basic information

species Glycine max
transcript GLYMA14G39050.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G39050.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 5'ss of exon 4
CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttactctt--cagaaatatttggaacaaaatacttgtagaatgtgaagtttacttctcccattatcaccattgtggtgtt----
||||  | ||  | || ||||| || ||||| |||| |||||| ||||| || ||||||||||| ||||| || || |||||| | || |||||||||||||||||    |   |  | | || |||  |      ||  | | ||||| |||    | | | | |  |||| |||  ||| | ||    |||| |  | |     
CACCCGAGTCGAAGGCAACAACTGAAAGTGTGTACAGTGCTGCTTTGGCTCTCGGCATTGCAAACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGAgtaagtgtcaatacagtggttttcactaatggtcataagctgtagaacagaatgtcggcata-tatatagttcactgatcctaatact-tcattttattttcacag

upper sequence: GLYMA14G39050.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 1
CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttactcttcagaaatatttggaacaaaatacttgtagaatgtgaagtttacttctcccattatcaccattgtggtgtt-
|| |  | ||  |||| ||||| || || ||||||| |||||||||||| || || ||||| || || || || ||||||||| | ||||||||||||||||||||     |  ||  || ||    || | || |     | |     ||   |  |  |    |  | |  |  |   | | ||||||| ||  | |  
CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagt-----aacatatatattcttcctgc-gacaggcacgaacatgcatgtgttcaatagcacagatgtgatgatatgactgtcaccat-gtcttttag

upper sequence: GLYMA14G39050.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G300348_T03 (Zea mays), 5'ss of exon 4
CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttactcttcagaaatatttggaacaaaatacttgtagaatgtgaagtttacttctcccattatcaccat----tgtggtgtt-----
|| |  | ||  |||| ||||| || || ||||||| |||||||||||| || || ||||| || || || || ||||||||| | ||||||||||||||||||||     |  ||  || ||    || | || |     | |     ||   |  |  |    |  | |  |  |   | | |||||||    | | ||| |     
CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagt-----aacatatatattcttcctgc-gacaggcacgaacatgcatgtgttcaatagcacagatgtgatgatatgactgtcaccatgtcttttagtgctagaag

upper sequence: GLYMA14G39050.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G17230.1 (Arabidopsis thaliana), 5'ss of exon 5
CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttact----cttcagaaat---atttggaacaaaatacttgta---gaatgtgaagtttacttctcccattatcaccattgtggtgtt----------------------------------------
  || || ||  |||| ||||| || ||||| ||||| |||||||||||||| || || || |||||||| || |||||||||||||| || || || |||| ||||  |   |||  || || | |    |||  |       ||||   | |    ||||  |   |  | |  | || || |    | ||   |||  | |  || |                                        
ATCCTAAGTCGAAAGCAACAACCGAAAGTGTTTACAACGCTGCCTTGGCCCTTGGTATAGCCAATCAGCTTACTAACATACTCAGAGACGTAGGCGAAGAgtgagtcttt--ttatatattttaaatagagctttggtttcttgatttcacatatctcacttaaaccggtttcttgatttcacatgcttcttttaaaccggtttcttgattcacatatctctcttaaattggttttgttctcactatcag

upper sequence: GLYMA14G39050.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 5'ss of exon 5
CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttactcttcagaaatatttggaacaaaatacttgtagaatgtgaagtttacttctcccattatcaccattgtggtgtt-
||||  | || || || || || |||||||| || || || ||||||||  |||| || ||||||||||| || ||||||||||| ||||||||||| ||||||||  | | ||||  |    ||  ||       ||| |   | |   | |         | |||   |   |   | | |   ||  | |     || 
CACCTGAATCACAGGCAACCACGGAGAGTGTCTATAAGGCAGCCTTGGCATTAGGGATCGCAAATCAGCTGACTAACATACTCAGGGATGTTGGAGAAGAgtaagtaaaaagctataaaaaaataa-ctgtgtgcctatgtcacatatgcttccctagaggagagaaaaatggataaacaaatgaaacattagaaaacttg

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|193711203|gb|FK643840.1|FK643840
EST:     CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGA                         TGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
genomic: CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccat ... ttttcaacagTGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
EST: gi|193679336|gb|FK619756.1|FK619756
EST:     CTAGGAATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGA                         TGCTAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
genomic: CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccat ... ttttcaacagTGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
EST: gi|13790571|gb|BG653162.1|BG653162
EST:     CAGAGATGTTGGAGAGGA                         TGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
genomic: CAGAGATGTTGGAGAGGAgtaagtccat ... ttttcaacagTGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
EST: gi|192307399|gb|FK000755.1|FK000755
EST:     CTAGGCATTGCAAATCAGCTAACCAACATATTCAGAGATGTTGGAGAGGA                         TGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
genomic: CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccat ... ttttcaacagTGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
EST: gi|7691635|gb|AW759759.1|AW759759
EST:     CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGA                         TGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
genomic: CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccat ... ttttcaacagTGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
EST: gi|192307398|gb|FK000754.1|FK000754
EST:     CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGA                         TGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG
genomic: CTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccat ... ttttcaacagTGCCAGCAGAGGAAGAGTGTATCTTCCACAAGATGAGTTGGCTCAAGCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttactcttcagaaatatttggaacaaaatacttgtagaatgtgaagtttacttctcccattatcaccattgtggtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA