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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatgttttctacagtttgcttctcgttatctgtacttctctttattatgcttagaatgcgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgagttaaagcaaaatagtggataaaaaattgtattatctgtacag

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 4
GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatgttttctacag-tttgcttctcgttatctgtacttctctttattatgcttagaatgcgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgagttaaagcaaaatagtggataaaaaattgtattatctgtacag
| | || || ||||||||||||||||||||| |||| |||||  |  |  | || ||||| || |||||||||||||| |||||||||||||| || ||||| ||   | ||||  | || ||  ||| | |   | || |||     ||| ||  |    | |||   || ||| |||   | | |   || |  ||  | |||   |  || ||  | | |   |                                                     
GGCTGCCGCTAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGCCTCATGTCTACTCCAGCTGTATCTGCTGTTATCCGTGAAAGAGTTGGTGCAGATgtaagatttattttacaaagattaactttttgcagtgtg-actg----ttagtactc----actgc---ttattttctctgtgttaacaaattaccttactggtgctttatcaaatcatcaaaaaatag---------------------------------------------------

upper sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G109383_T01 (Zea mays), 5'ss of exon 4
GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatgttttctacagtttgcttctcgttatctgtacttctctttattatgcttagaatgcgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgagttaaagcaaaatagtggataaaaaattgtattatctgtacag
| | || || ||||||||||||||||||||| |||| |||||  |  |  | || |||||||| ||||||||||| || |||||||||||||| || ||||| |||    |||   | |     | | || ||| |  ||      |||| | || |   | | | ||       || | | || || | ||| | |     |  ||   |||  |  || |                                                         
GGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAAGAGTTGGTGCAGATgtaagttggatttctaataaaggacat-tctttagcaatatgaacatttact-tgtt---actcctttacaccgtctaataaattatacctgactattggtttataaacacatg-gacaatag--------------------------------------------------------

upper sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatgttttctacagtttgcttctcgttatctgtacttctctttattatgcttagaatgcgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgagttaaagcaaaatagtggataaaaaattgtattatctgtacag
| ||||||| ||||| || |||||||| ||| ||||||||||  |  |||| ||||||||||||||||| ||| |||| ||||||||||| || |||||||||||  ||  || ||  |   |  | ||  |||  | |   |    || |||| || ||  |  |  | |||| |   || |||    ||||  |  ||     | |  |    | |   ||||                                                      
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatat-cttcctctaaactcatactacttacttttctcttgggttgttat-ctaaggctatgcat-gtttgc---aacatg--taatgacgtg-atgagaaactaacccgagatccaatttcag---------------------------------------------------

upper sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 5
GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatgt--tttctacagtttgcttctcgttatctgtacttctctttattatgcttagaatgcgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgagttaaagcaaaatagtggataaaaaattgtattatctgta--cag
| |||| ||||||||||| |||  ||| ||| ||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||||| ||    ||||| |||||| |   ||| ||  | | | |||   | | ||| |||||          |   | | |          || | |   | ||   | | |   || ||    |||||  | | || |  ||        |||   ||  |||||| || ||    |  |||| ||| |  |  |||
GGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGTCAAAATGGGTTGCTTTCAACTCCTGCTGTATCAGCTGTCATCCGTGAAAGAGTGGGGAAAGATgtaagtaatttggcttcaactatctacatcttactgtatgtccttcttcgc------cgccgcacgtccccccacccccccagtttcatttttaaat---attgtttgcttgcagttaggaataggtt--------gagaacaacaaaaataatgaatttgtatatgtactatattaaatcag

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|254347113|gb|GR856783.1|GR856783
EST:     TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|151396774|gb|EV266647.1|EV266647
EST:     TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|209696727|gb|BW672906.1|BW672906
EST:     TTTCTACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|213611739|gb|DB958861.1|DB958861
EST:     TTTCTACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|213617812|gb|DB967258.1|DB967258
EST:     TTTCTACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTG
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTG
EST: gi|7146923|gb|AW508845.1|AW508845
EST:     TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|213605046|gb|DB956379.1|DB956379
EST:     TTTCTACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|15285957|gb|BI469848.1|BI469848
EST:     TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|6070595|gb|AW099982.1|AW099982
EST:     TTTCAACTCCTGCAGTATCTGCTGTTATACGTAAAAGAGTTGGAGCTGAT                         GGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCCAGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGGT
EST: gi|7684820|gb|AW755468.1|AW755468
EST:     TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGAT                         GGATCCCAGG-CAACAGGTGCATNTATACTGACAGCAAGTCACAATCCTGG
genomic: TTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatg ... atctgtacagGGATCC-AGGGCAACAGGTGCATTTATACTGACAGCAAGTCACAATCCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatgttttctacagtttgcttctcgttatctgtacttctctttattatgcttagaatgcgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgagttaaagcaaaatagtggataaaaaattgtattatctgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT