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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaaccaataccttatgtattttagataagcctcaaattctttctcttcatgctaattgtcatcatagctacgacaatcaccatcatacatgcttctcatatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG

Basic information

species Glycine max
transcript GLYMA16G27220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G170595_T01 (Zea mays), 3'ss of exon 3
gttagaaccaataccttatgtattttagataagcctcaaattctttctcttcatgctaattgtcatcatagctacgacaatcaccatcatacatgcttctcatatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
           ||   | ||||| | |    || ||| || | |||      ||  | ||       |  |||  |  |    | ||   | |     |  |     | | ||| |||||||| || || || ||||| ||||| || |||||||| || |||||||||||||| || || ||| | || ||||| |||||||||||||| |
---------gttagtgtctgtatctca----agactccaactttttgctgatatcttcatc----caaaggctgagttatcgtctatttcataaatggcgga-----attgcagATGTGTGCTTGAACCAGGCGACAAAATTGTTGATTGCCCTCCAACATTCACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG

upper sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 4
gttagaaccaataccttatgtattttagataagcctcaaattctttctcttcat--gctaattgtcatcat--agctacgacaatcacca-tcatacatgcttctcata------------tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
|||||||     |  || ||| ||| |  | ||| | ||| |  |  |  || |  | |  | ||    ||  |  |    ||||  ||| |  |  ||  |  | ||             | || | ||| ||||| ||||||||||| |||||||||||||| || || || || |||||||||||||||||||||||||| |||||||| ||||||||| ||||||
gttagaaatggaagattttgtgttt-acttgagctttaaaattatattgatctttggtttgtagtttctatttaattctaccaattcccaattgtttattttgtttattattgcattgacctctattacagATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG

upper sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g02170.t01 (Vitis vinifera), 3'ss of exon 2
gttagaaccaataccttatgtattttagataagcctcaaattc---tttctcttcatgcta-attgtcatcatagctacgacaatc----accatcatacatgcttctcat-atat----------actccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
|||||||     |  || | | ||| |  | | | | ||| |    ||  ||||||   |  | | ||    ||  |     |||     |  ||   |  || || | ||   ||          | | ||| ||||| |||||||||||||||||| ||||||||||||| || |  |||||||||||||||||||||||||| |||||||| ||||||||| ||||||
gttagaaatggaagattttttgttt-acttgatctttaaaattatattgatcttcagtttgtagtatctatctaattctagtaattcctaattatttaatttgtttgttatcgcattgacttcctgattacagATGTGTACTGGATCCTGGAGACAAGGTTGTGGACTGCCCGCCAATTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAG

upper sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
lower sequence: EDP01242 (Chlamydomonas reinhardtii), 3'ss of exon 1
-----------------------gttagaaccaataccttatgtattttagata--agcctcaaattctttctcttcatgctaattgtcatcatagctacgacaatcaccat-catacatgcttctc-atatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
                          || |  ||   |    | | |    ||   |    |  ||     ||  |  |   |||        |    | |       |    |  ||  |||  || |  |   |    | ||||||||||| || || |||||||| ||||||||||| || |||||||| ||                                            
cagccaaccccacaccgcgacggaccagcaggaaaggccaccgcactcgtaatgccatttgcttatcaacactactactaacaatgacggctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTGGAGCCCGGTGACAAGATCGTGGACTGCCCGCCCACCTTCACCAT--------------------------------------------

upper sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ31551 (Selaginella moellendorffii), 3'ss of exon 3
gttagaaccaataccttatgtattttagataagcctcaaattctttctcttcatgctaattgtcatcatagctacgacaatcaccatcatacatgcttctcatatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
                             ||||      |     ||    | ||||  || |  || |   | |     ||  ||  | |   | |  |||| |   ||  ||||||    ||||   ||| |||||||||||||| || ||||| || |||||||||||||  |||||||| || || || ||||||   || |||||||
----------------------------gtaagt----gaacgactcctagcgtgcttttttttttctt--ttgc-----tcttcacgagatg-gttcttcatct---ctttagTTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAG

upper sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ04411 (Selaginella moellendorffii), 3'ss of exon 3
gttagaaccaataccttatgtattttagataagcctcaaattctttctcttcatgctaattgtcatcatagctacgacaatcaccatcatacatgcttctcatatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
                             ||||   |  | || ||   ||  |  |  || || |      |       ||  ||  | |   | |  |||| |   ||  ||||||    ||||   ||| |||||||||||||| || ||||| || |||||||||||||  |||||||| || || || ||||||   || |||||||
----------------------------gtaagtgaccgactccttgcgttttttttttttttcttttccttt----tgctcttcacgagatg-gttcttcatct---ctttagTTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAG

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|193460633|gb|FK429194.1|FK429194
EST:     TGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|298171050|gb|HO016082.1|HO016082
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTCCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|209706878|gb|BW653144.1|BW653144
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCT
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCT
EST: gi|42723210|gb|CK769109.1|CK769109
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|254330364|gb|GR841629.1|GR841629
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|14126228|gb|BG790666.1|BG790666
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCT
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCT
EST: gi|192322955|gb|FK016686.1|FK016686
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|209716352|gb|BW650751.1|BW650751
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGGTCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|192325038|gb|FK016164.1|FK016164
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|18040723|gb|BM309017.1|BM309017
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGGGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCC
EST: gi|192325422|gb|FK018378.1|FK018378
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
EST: gi|193431465|gb|FK396091.1|FK396091
EST:     TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCG                         TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC
genomic: TATATTCTTGCAGGGTGTGGTGCAGATGAGCTTATTGATTTGATCATGCGgttagaacca ... tatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcatcatagctacgacaatcaccatcatacatgcttctcatatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
                                        tcatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaaccaataccttatgtattttagataagcctcaaattctttctcttcatgctaattgtcatcatagctacgacaatcaccatcatacatgcttctcatatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA