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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacctgatatctcag

Basic information

species Glycine max
transcript GLYMA19G27250.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g01307.1 (Oryza sativa), 5'ss of exon 4
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgta--tatttcctgtat-acttgaacttgacagt-tacatgaatcaata--tcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacct-gatatctcag
                            ||||| |||||||| |||||  |  |  | ||||||||| |||| || ||||| || ||||||||||||||||||  || ||     ||  | || || |   ||| |   |   || ||    | | ||   | ||| ||  |    |  |  | |      |  ||| |||||   || | |  ||| | |   ||||
----------------------------GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGGgtaagtaattgtgccattgcatgtacattctagtctgtttcgctctatgatcctaatgtgctgatgctgtttatgtttctggcatgcgccgtgtatgaattcttgatgttctctccttgttggttcag

upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G067476_T03 (Zea mays), 5'ss of exon 3
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacctga-tatctcag
       | |  ||| |     |   |||||||||| ||||||||||| || ||  ||||| ||||  |||| |||||||| |||||||||||||||||||||  |     | || |    | |  ||    |    | |  || |   ||||    ||  |||    |  ||    ||| || | | |     ||| | |||    | |||| |||     
----ATCAATGCTTTGTACATGTTGAAGGAGGCATACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACCTCCAGAGAAGAAGTTTGAATGGGTAAgtaa---gcatgcc---attgcacgcacaacctagttcatgtttcttgccc--atactgatgttcggatgctgtttctggtgttac---ctctgcgtgga--aatctgaatat-----

upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G067476_T02 (Zea mays), 5'ss of exon 4
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacctga-tatctcag
                            |||||||| ||||||||||| || ||  ||||| ||||  |||| |||||||| |||||||||||||||||||||  |     | || |    | |  ||    |    | |  || |   ||||    ||  |||    |  ||    ||| || | | |     ||| | |||    | |||| |||     
----------------------------GAGGCATACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACCTCCAGAGAAGAAGTTTGAATGGGTAAgtaa---gcatgcc---attgcacgcacaacctagttcatgtttcttgccc--atactgatgttcggatgctgtttctggtgttac---ctctgcgtgga--aatctgaatat-----

upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G067476_T01 (Zea mays), 5'ss of exon 4
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgtt-gactgacatatttactttttgttttcatgtattctacttggtttgacctgatatc----tcag
                            |||||||| ||||||||||| || ||  ||||| ||||  |||| |||||||| |||||||||||||||||||||  |   |  |    ||| ||   |||      |  ||   | |         | ||||| |  ||   | | |  | ||    |    ||      ||   | ||  || |||      ||||
----------------------------GAGGCATACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACCTCCAGAGAAGAAGTTTGAATGGgtaagtaagc-atgccattgcacgc-acaacctagttcatgtttcttgcccatactgatgttcggatgctgtttctggtgtt-acctctgcgtggaaatctgaatatgctctcatactatgttcag

upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G376727_T03 (Zea mays), 5'ss of exon 4
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacctga-tatctcag
                            ||||| || ||||||||||| || ||  ||||| ||||  |||| |||| ||| |||||||||||||||||||||  |   |   || |     | ||    ||  |    |  || |   ||  | | ||  |||       ||    ||| || |   |     ||| | |||    | |||| |||     
----------------------------GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAAgtaatc---atgccattgcatgcgcattgta---gttcatgtttctt--tctgatactgatgtttggatgctgtttctggtgctac---ctctgcatgga--aatctgaatat-----

upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 4
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatt-tcctgta--tacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgtttt-catgtat-tctacttggtttgacctgatat-ctcag
                            ||||| || ||||||||||| || ||  ||||| ||||  |||| |||| ||| |||||||||||||||||||||  |  || ||    | | ||  | |   |||| ||||  ||  | ||   | ||  | | |||  ||   | | |  |  |   | | |||| |  |||   |    |  | |  |||  ||||
----------------------------GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatcatgccattgcatgcgcattgtagtt-catgtttc--tttctgatactgatgt-ttggatgctgtttctggtgctacctctgcatggaaatctgaatatgctctcatactatgttcag

upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G376727_T02 (Zea mays), 5'ss of exon 4
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacctga-tatctcag
                               || || ||||||||||| || ||  ||||| ||||  |||| |||| ||| |||||||||||||||||||||  |   |   || |     | ||    ||  |    |  || |   ||  | | ||  |||       ||    ||| || |   |     ||| | |||    | |||| |||     
-------------------------------GCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAAgtaatc---atgccattgcatgcgcattgta---gttcatgtttctt--tctgatactgatgtttggatgctgtttctggtgctac---ctctgcatgga--aatctgaatat-----

upper sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0068g01370.t01 (Vitis vinifera), 5'ss of exon 4
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacctgatatctcag
                            ||||||||||||||||| ||||| ||||| ||| | ||| | |  |||||||| |||||||||||||| ||||||  |||||  ||      ||  |  |||||| || ||||| ||||      |||||||       || | |||   | |||  || | |  || |  ||| |||  | ||  ||     
----------------------------GAGGCATATTCAACTCCAATATTACCTTTAGATATCCTTGCAGTGAGACCTCCAGAGAAGAAGTTTGAGTGGgtaagtttcccata------aaagtagcagttatattaatcattatc-----tttttatgc------acctttttctgtgttgacttaa-gccttttctttgtttttccatggaatta---

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|209706550|gb|BW667815.1|BW667815
EST:     TGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcc ... gatatctcagGCTAAG
EST: gi|193559196|gb|FK512063.1|FK512063
EST:     CGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: CGAGAAGAAGTTTGAATGGgtatatttcc ... gatatctcagGCTAAG
EST: gi|58015600|gb|CX702342.1|CX702342
EST:     CCTCCCGAGAAGAAG-TTGAATGGG                         GCTAAG
genomic: CCTCCCGAGAAGAAGTTTGAAT-GGgtatatttcc ... gatatctcagGCTAAG
EST: gi|31455985|gb|CD398013.1|CD398013
EST:     GTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: GTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcc ... gatatctcagGCTAAG
EST: gi|213604354|gb|DB983470.1|DB983470
EST:     GCCTTTGGATGTTC-TTCTAGATAGACCTCCCGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: GCCTTTGGATGTTCTTTCT-GATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcc ... gatatctcagGCTAAG
EST: gi|18039442|gb|BM307736.1|BM307736
EST:     TTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcc ... gatatctcagGCTAAG
EST: gi|193364946|gb|FK333203.1|FK333203
EST:     GAAG-TTGAATGG                         GCTAAG
genomic: GAAGTTTGAATGGgtatatttcc ... gatatctcagGCTAAG
EST: gi|193709620|gb|FK646000.1|FK646000
EST:     ACCTCCCGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: ACCTCCCGAGAAGAAGTTTGAATGGgtatatttcc ... gatatctcagGCTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatttcctgtatacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgttttcatgtattctacttggtttgacctgatatctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT