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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattactttgtttgatcttggattttgacatttgcaagtcattcattctttaacaaactccacttgttgtcaattggctaatg...

Basic information

species Glycine max
transcript GLYMA04G02100.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattactttgtttgatcttg-gattttgacatt-tgcaagtcattcattctttaacaaactccacttgttgtcaattggctaatg
|||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||| || || ||||| || || || ||||| || || || ||||||||||  ||   | ||| |   ||  | | |  |  | || | | |||   || |||||    || |    |     | ||    | |||  ||           
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta-gtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgt--gtgagcttacatggtttgcag----------

upper sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G126361_T03 (Zea mays), 5'ss of exon 4
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattactttgtttgatcttggatt-ttgacatttgcaagtcattcattctttaacaaactcc-acttgttgtcaattggctaatg----
|||| |||||||| |||||||| |||||||| ||||| || |||||||||||||| || || || ||||| || || |||||||| ||||| ||||| ||||  |  |    ||||    |||| ||||   |  || ||  |||||  ||||   |  | |     || |   |||   |  |||  ||   ||| |        
GTGGACTCACATTCTTTGCTCCAAGCGAAGAAAGGCTAGAATCTGGATTGTACAGCAGGAGCTATCTTGAGAACCAAATGGCTGTAGCCCTTGGTGGCAGgt--gctctttctgca----tactctgttcatttctgcatcattgactgttgc---tgctgcgcatattgatggactgtgagatgtaatcttatggtttgctgcag

upper sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagt--gcaacgtgcacaattactttgtttgatcttggattttgacatttgcaagtca---ttcattc---tttaacaaactccacttgttgtcaattggctaatg----
|||| ||||| ||||||||||| |||||||| || || |||||||||||||||||||| || |||||||| ||||| ||||||||||| || || ||||||| |||  | || |  | | |   ||       |       | ||   || | ||    |   || | |    || ||| | ||| |  | |  |   ||||||| ||    
GTGGGCTCACTTTTTTTGCTCCAAGCGAAGAAAGACTTGAGTCTGGATTGTACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAGgttagttagtaatggcctccacgcctcgtcacaaaagccagtctttgaatatacagagaagggtttaattatgttaaaccatctctatctctgttgtgttggcta-tgtcag

upper sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattactttgtttgatcttggattttgacatttgcaagtcattcattctttaacaaactccacttgttgtcaattggctaatg
|||| ||||| ||||| ||||| |||||||||||||| ||||| |||||||| || ||||| |||||||| || || ||||||||||| || ||||||||||   |   |  || |    ||||   |||||| |   |   |    || |   || |  || | ||||      | ||| | | ||             
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag-----------

upper sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattac-tttgtttgatcttggattttgacat-ttgcaagtcattcattctttaacaaactccacttgttgtcaat--tggctaatg--
||||||| || ||||||||||| || |||||||| |||||||||||| ||||||||||||||||||| || ||||||||||||||||| ||||||||||||| |||      |||  |||  | | |    || |    |  | |   | ||  |  || |    ||||| |  ||  | | ||  ||  |||  |  ||   |  
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagt------tgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat

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|209723842|gb|BW675213.1|BW675213
EST:     AGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: AGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120494712|gb|EH222879.1|EH222879
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|214008784|gb|DB989600.1|DB989600
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGTTAGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCAACGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120494290|gb|EH222457.1|EH222457
EST:     TACAGTAGAAGTTA-CGTGGAAATCAGATGNCTGTTGGCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209720268|gb|BW674610.1|BW674610
EST:     CTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: CTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209708483|gb|BW668315.1|BW668315
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120494704|gb|EH222871.1|EH222871
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGGCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209698096|gb|BW661039.1|BW661039
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|192306887|gb|FG999934.1|FG999934
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120494410|gb|EH222577.1|EH222577
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209707248|gb|BW670579.1|BW670579
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120495954|gb|EH224121.1|EH224121
EST:     TACAGTAGAAGTTACCTTGAGAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120494718|gb|EH222885.1|EH222885
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209709685|gb|BW657214.1|BW657214
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|214008460|gb|DB986721.1|DB986721
EST:     CTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: CTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120495724|gb|EH223891.1|EH223891
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|9984609|gb|BE658717.1|BE658717
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209727706|gb|BW658443.1|BW658443
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120529263|gb|EH257397.1|EH257397
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120494207|gb|EH222374.1|EH222374
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120493960|gb|EH222127.1|EH222127
EST:     ATCAGATGGCTGTTGACCTGGGTGGAAG                         GTTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: ATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|192306886|gb|FG999933.1|FG999933
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|16282177|gb|BI944877.1|BI944877
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|214007663|gb|DB986029.1|DB986029
EST:     CTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGTCGAAGAGGTTATTTTTGGCCAGGAAAATGTCAACAGCGGAGCATC
genomic: CTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209708811|gb|BW673873.1|BW673873
EST:     AGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: AGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|120495615|gb|EH223782.1|EH223782
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|208307941|gb|GE108445.1|GE108445
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTT
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattactttgtttgatcttggattttgacatttgcaagtcattcattctttaacaaactccacttgttgtcaattggctaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG