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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA

Basic information

species Glycine max
transcript GLYMA17G13440.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
|||||||  | |   |  |||  |   |    |   |||     || |     |||| |      | | ||  |||    ||   ||||| | ||| ||||||||||| || ||||| |||||||||||||| |||||||| |||||| ||||||| || |||   | |||| | || || |  ||
gtatgtt--gttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttt------tgagttacgaaagc-taccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA

upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
               |    |  |||           |||| | ||| |   ||     |     | | ||   ||    |  | ||||| |  ||  | || |||||||||||||| ||||| ||||| || |||||||| ||||| ||||| || || ||| | |  ||||| ||||| |  ||
--------------gtatgttattgtgccttggtttgattt-tgcatgtacaagtacagaggatctgagttaccaag--gttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA

upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagatt--ctattccataatttgtga---atttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
||| ||||   |   | || | |  |  |       | ||| |       || || |    |    || ||     |   ||| ||   |||||| | ||| |||||||||||||| || ||| ||||||| ||||||||||||||||||||  | |||||| | || |||| |||| |||||||||| ||
gtacgttta-ttaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA

upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------gtatgtttggc----tctctcaaatcct-gtataaaaaacatatttatccatctct---tagattctattccataatttgtgaattta-tattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
                                                                                |||  ||||      ||| | |  || | || |   |  |  |  | |  |   |    || ||  | |||  |  ||   | ||||  |||  ||||| |  || ||||||||||||||||| |||||||||||| | || ||||||||| | ||  | |||||  | ||    | |||| | ||||| |  ||
gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttgctatggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGA

upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
                           ||| |||  |    |    ||  |||      ||  |||| ||  ||  |     || ||||| |   | ||||||||||||||||||||| | ||||| || || |||||||||||  | || |||||  | ||    | |||  |  | |  || ||
--------------------------gtaagaaaactgcaaa---gtccatta------atctcatatttcttggctgc---ttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ32324 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
                           ||| |||  |    |    ||  |||      ||  |||| ||  ||  |     || ||||| |   |  |||||||||||||||||||| | ||||| || || |||||||||||  | || |||||  |  |    | |||  |  | |  || ||
--------------------------gtaagaaaactgcgaa---gtccatta------atctcatatttcttggctgc---ttccagGGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTTCCAGACGCATAATCGATAACGTAGA

upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ20930 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
                           ||| |||  |    |    ||  ||   | | ||   ||| ||  ||  |     || ||||| |   |  |||||||||||||||||||| | ||||| ||||| |||||||||||  | || |||||  | ||    | |||  |  | |  || ||
--------------------------gtaagaaaactgcaaa---gtccattgattccaatcttatatttcttggctgc---ttccagGGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTTGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

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|193703915|gb|FK634803.1|FK634803
EST:     TGATATCTAGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: TGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|9204054|gb|BE330278.1|BE330278
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|151400202|gb|EV270016.1|EV270016
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|21602499|gb|BQ612830.1|BQ612830
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|15813777|gb|BI786052.1|BI786052
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|23728459|gb|BU762283.1|BU762283
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGGCTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|207847382|gb|GD820423.1|GD820423
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|208051460|gb|GD845927.1|GD845927
EST:     GGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: GGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|151400815|gb|EV270629.1|EV270629
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
EST: gi|208123639|gb|GD924541.1|GD924541
EST:     ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG                         GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG
genomic: ATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttgg ... tatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA
                         tattccataatttgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA