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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgtttgaccattgctattatacgaataagacttgtcctgcacttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG

Basic information

species Glycine max
transcript GLYMA10G32660.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
----taatgtttgaccattgctatt-atacgaataagacttgtcctgcacttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
    | || ||       ||||||| ||    | |    ||    |  |      |   || |     |  || | | |   | ||| |   || ||    ||||||||||  | || ||  | || ||||| ||||| || |||||||| ||| | ||||| |||||  |||| ||||| ||| ||||||||||||||||||||
cttgtcatattatgtgcatgctatttatctagaaacagattacattatagac--accatttgacaaactccatataattcctttgtaatgctacttac---acagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG

upper sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G062416_T04 (Zea mays), 3'ss of exon 1
taatgtttgaccattgctattatacgaataagacttgtcctgcactt--ttgcttcttaattgcattgatgttaa-tgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
    | |||    |   | ||  |    | |  |  ||||  || |     |   ||||  ||  | | ||| |  || |  | |  ||   || |||||  ||||  | ||||||||  |  | ||||  || |||||| ||||||| ||| ||||||| ||||||||||| | ||| ||  |||||||| | |||||||||
-gggggttgttattatttgtttgaaatctgattcaggtcccacattcaaccgggccttatgtgattagttgtaagctgacatgaagatgatgcttttgta--gGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG

upper sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 5
taatgtttgaccattgctattata-cgaataagacttgtcctgcacttttgcttcttaattgcattgatgttaat-gtctagtatttg-gacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
    |  ||  | |  | |  ||| |   | | ||||| | |  | |||   || ||  | ||  | |||| ||| ||||| |  |   | | |    | ||||||||||||||||||| |  | ||| | || || || ||    || || || || |||||||||||||||||||| ||||| || ||| | |||||||||
--cagactgttcttaacaaacatagcttcttacacttg-catctattttacttttttcttcgctgtaatgtaaattgtctacttctgatggcttccaatgcagGTTTCTTCTCCCAGCATCTTTAATTATAATCAACGACATCTTCGCCTACATTTTCGGTTTCTTCTTTGGAAGAACGCCTTTAATAAAGCTGTCTCCAAAG

upper sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 4
------------------taatgtttgaccattgct-attatacgaataagacttgtcctgca--cttttgcttcttaattgcattgatgttaa-----tgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
                  ||| | ||     ||| |   |    |  ||   |||||  |     || |||  ||||  ||          |||     | | || |||   |     | || |||||||||||| || ||| ||||||| ||||| ||||| ||   ||| ||||||| ||||||||||||||||||||| || |||||||||||||| ||||||
gtagtcacctattccttttaacgcttcttacttgtttgctccgtgtttagttcttgtgttattttctcttgtatcttggttatgacctgactaaaagtctatttactatactggttgctggtgcagGTTTCTTCTTCCTGCATCACTTATCGTCATCAATGACATATTTGCATATATCTGTGGTTTCTTCTTTGGAAGAACACCGTTGATCAAGTTATCACCAAAG

upper sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 5
-taatgtttgaccattgct-attatacgaataa--gacttgtcctgcacttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
      |||| || || ||   |    || | |  |  |||||  |   ||    ||||| |||   || || ||  || |     || | | | ||    |||||||||||| |||||| |||||||||| || |||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||| 
aaggactttgccctttacttgattcttgagtgattggattgtcaagtctttggaattctttatt-tgtttattttcctgacatagtttagtatcaat---gcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACACCTTTGATTAAGTTATCTCCAAAA

upper sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 5
-taatgtttgaccattgct-attatacgaataa--gacttgtcctgcacttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
      |||| || || ||   |    || | |  |  |||||  |   ||    ||||| |||   || || ||  || |     || | | | ||    |||||||||||| |||||| |||||||||| || |||||||||||||||||||||||||                                            
aaggactttgccctttacttgattcttgagtgattggattgtcaagtctttggaattctttatt-tgtttattttcctgacatagtttagtatcaat---gcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATATCTTTG--------------------------------------------

upper sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 6
taatgtttgaccattgctattatacgaataagacttgtcctgcacttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
                                                 | |||||  |||    || |  ||   ||  |  ||                        || || || |  | || ||||||  ||  | ||  ||||   ||                                               
-------------------------------------------------gtttcttctttg----gaag--aacacctt-tgattaagttnnnnnnnnnnnnnnnnnncccaagtaaaaactgttttcatta--gac-tagCAACTTACTACTCG---------------------------------------------

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|13480063|gb|BG509406.1|BG509406
EST:     TTTGGCCAGTCCTCCTTCACCGTGGCAAGCATTTTTGAAGGGATTTTCTG                         GTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATAT
genomic: TTTGGCCAGTCCTCCTTCACCGTGGCAAGCATTTTTGAAGGGATTTTCTGgtaatataac ... tattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATAT
EST: gi|31561270|gb|CD487108.1|CD487108
EST:     TTTGGCCAGTCCTCCTTCACCGTGGCAAGCATTTTTGAAGGGATTTTCTG                         GTTTCTTCTCCCAGCAAGACTTATTGTCATTAATGATATTGCTGCTTATAT
genomic: TTTGGCCAGTCCTCCTTCACCGTGGCAAGCATTTTTGAAGGGATTTTCTGgtaatataac ... tattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATAT
EST: gi|17153399|gb|BM143332.1|BM143332
EST:     TTTGGCCAGTCCTCCTTCACCGTGGCAAGCATTTTTGAAGGGATTTTCTG                         GTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATAT
genomic: TTTGGCCAGTCCTCCTTCACCGTGGCAAGCATTTTTGAAGGGATTTTCTGgtaatataac ... tattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
                      tgttaat  putative branch site (score: 3)
      ttcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgtttgaccattgctattatacgaataagacttgtcctgcacttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- atgtttg
- - - - - ccattgc
- - - - - - - - - - - - - - - - - -tgtcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg