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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctggcacaaattgttgccattcatatcatctatgccctttttgtagttcaaatggttttaatctgaatttaatgtctatgaatttgctttgtcttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG

Basic information

species Glycine max
transcript GLYMA03G32620.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
gctggcacaaattgttgccattcatatcatctatgccctttttgtagttcaaatg-gttttaatctgaatttaatgtctatgaatttgctttgtc-ttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG
  ||       || ||  | | || | |  ||      |  |  || ||    |    | ||| |  || |     ||| |   |||  ||| |   |||||||||| | ||| ||||||||||| ||||| || |||||||||||||| ||||| || |||||||| |||||||||||||||||  | || || || || |
aatgatttgc-ttattatcctccacaactact-catattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

upper sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12
gctggcacaaattg-ttgccattcatatcatctatgccctttttgtagttcaaatggttttaatctgaatttaatgtctatgaatttgctttgt--cttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG
      | || ||  ||   || |   ||| |||  |   | |||    |    ||  |  ||| | | |  |||    ||    ||  ||| |  |||||||||||| | ||| ||||||||||| ||||| || ||||||||||| || ||||| || || ||||| ||||||||||||||||   | || || || || |
-tcaaaataatttacttattatcctcctcaacta--ctaatattgctcatactttgtgtacaatgtaagtcaaattatcattttcttcatttattacttttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG

upper sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------gctggcacaaattgttgccattcata----tcatctatgccctttttgta-gttcaaatggttttaatctgaa-tttaatgtct-atgaatttgctttgtcttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG
                                       ||| ||  |   |  ||| |   |    |  || |   | || || |  ||||||||  |  |  |||||  ||| | |||| |     |   ||||||  | |||| |||  ||| |||||||||||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||||||||||||  |||| ||||| || |
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

upper sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
---------------------------------------------------------gctggcacaaattgttgccattcatatca--tctatgccctttttgtagt---tcaaatggttttaatctgaatttaatgtctatgaatttgctttgtcttt-tagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG
                                                          ||   | ||| | |  |  |  |  |||  |||||   | |  |  | |   | || |  ||||| |  |     ||   || |   | |  | ||| ||   |||| |||| ||| ||||||||||| ||||| |||||  | |||||||| ||||| ||||| |||||||| |||||||||||    | ||| || || || |
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttggg--ccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

upper sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------gctggcacaaattgttgcc-attcatatcatctatgccctttttgtagttcaaatggttttaat--ctgaatttaat--gtctatgaatttgctttgtctttt-----------agGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG
                                                          |    ||   || || |  | ||  |   |  ||| |  || |  | | | | | |  || ||  || ||| |     | ||| | |   | ||| ||||||           ||||||||| ||| ||||||||||| ||||| || || ||||| ||||| || || || || |||||||| || ||||||||    | ||| || || || |
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG

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|193349420|gb|FK316536.1|FK316536
EST:     GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAG                         GTAATAACAAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCA
genomic: GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAGgtaaaatgaa ... tgtcttttagGTA-TA-CAAA-GTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCA
EST: gi|10708953|gb|BF008738.1|BF008738
EST:     GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAG                         GTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAGgtaaaatgaa ... tgtcttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|9565407|gb|BE474916.1|BE474916
EST:     GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAG                         GTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAGgtaaaatgaa ... tgtcttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|7588238|gb|AW704038.1|AW704038
EST:     GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAG                         GTATACAAAGTGTCAGATATGGAACTTTGTAAGG-TGCTTGCTAGTGCAGA
genomic: GTATTGTTATCGATGGAGAAACAACATTGCCTATATATACAGTGTTAGAGgtaaaatgaa ... tgtcttttagGTATACAAAGTGTCAGATATGGAACTT-GTTAGGGTGCTTCCTAGTGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcaaatggttttaatctgaatttaatgtctatgaatttgctttgtcttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG
                                      tttgctttgtctttt  CT-rich tract
           ttttaatctgaattta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctggcacaaattgttgccattcatatcatctatgccctttttgtagttcaaatggttttaatctgaatttaatgtctatgaatttgctttgtcttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA