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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttctttgtgataagctactttgtgcctgacctaagaataccatttctgaaattgactttattcattcaaaaatcag

Basic information

species Glycine max
transcript GLYMA10G06580.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagttt--aatcttgtgatttgtctc-ctcctttctttgtgataagctactttg-tgcctgacctaagaataccattt--ctgaaattgactttattcattcaaaaatcag-----
|||||||||| | || ||||| |||||||| || |||||||| |||||||| || ||||| |||||||||||||||||      |   | |||||| |  || ||||   |||||     | | |||| ||| |||   ||  ||  | | |  |  |  |  ||    |  |  ||  |  || |  | | |||  |     || |     |     
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag

upper sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g43750.2 (Oryza sativa), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttctttgtgataagctactttgtgcctgaccta-agaataccatttctgaaattgactttattcattcaaaaatcag
             || ||||| |||||||| || |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| || | |||||  |  ||    ||| | |  |   ||  ||    |    | | |  |  || |  |  |  |   ||  |      ||||| |||     |  |||  |||
----------ATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAATgcaagttataagttcctctttatgttttaaatttcttccatttttatgcctcttcactcagttgcaccactgcacatactgccttgaccttaccatctttaaa--cag

upper sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttctttgtgataagctactttgtgcctgaccta-agaataccatttctgaaattgactttattcattcaaaaatcag
|||||| ||    || ||||| |||||||| || |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| || | |||||  |  ||    ||| | |  |   ||  ||    |    | | |  |  || |  |  |  |   ||  |      ||||| |||     |  |||  |||
GATGCTCCAGATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAATgcaagttataagttcctctttatgttttaaatttcttccatttttatgcctcttcactcagttgcaccactgcacatactgccttgaccttaccatctttaaa--cag

upper sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttctttgtgataagctactttgtgcctgacctaagaataccatttctgaaattgactttat-tcattcaaaaatcag
|||||||||| | || ||||| |||||||| || || ||||| ||||||||||| ||||| ||||| |||||||| ||     | ||  | | || |   || | | | |  || | || |   |  || |    ||    ||  |   |||||  |  |  ||    |    |  || | || | ||| || || |   | | ||||
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGAAAGGACAAGTTTGGTGAGGAAATGAAGAAAAA-----CGCTCAA-GCTGCAGGAGTTACTgttagtttttaatct-cattgtcttcatgttactttagacagttttgttgc-aatttattggttaattcactcatatggccttgatgtcgtcgcatactcag

upper sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAA-ATGTACACTAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttct-ttgtgataagctactttgt-gcctgacctaagaataccatttctgaaattgac-tttattcattcaaaaatcag
|||||||||| | || ||||| |||||||| || || ||||| || |||||||| ||||| |||||||||||||| ||     |  ||  | |   ||  | ||  ||||||||  |  | |   | || ||||     || ||   ||  ||| | | || |   |  |||      | |||  ||| |  |||   | |||        
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGGAAGGACAAGTTTGGTGAGGAGATGAAGAAAAATGCTCAAGCTGCAGGAGTTACTgttagttttaatctcatcttcttcatgctactttagacagtaatgttctgatttattggctaattgactaatgtggcct-tgatgttggcgcttacctactcag-------

upper sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttctttgtgataagctactttgtgcctgacctaagaataccatttctgaaattga---ctttattcattcaaaaatcag
||||||||||   || || || ||||| ||||| || ||||| ||||||||||| ||||| ||||| |||||||| || |  | ||| | |||||| || ||||||||  ||   |  |||   || |       || |     | ||       |   |  | ||| ||    || ||  | |||   || |   || || |  |||||
GATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTAATgtaagttttttcacttc-tttacatcttttgcagcttttccatggttatccatctctccattttagattagttgttttgttactgagacctcttaacaatccatgatcag

upper sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttctttgtgataagctactttgtgcctgacctaagaataccatttctgaaattga---ctttattcattcaaaaatcag
||||||||||   || || || ||||| ||||| || ||||| ||||||||||| ||||| ||||| |||||||| || |  | ||| | |||||| || ||||||||  || | |  |||   || |       || |     | ||       |   |  | ||| |     || ||  | |||   || |   || || |  |||||
GATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTAACgtaagttttttcatttc-tttacatcttttacagcttttccatggttatccatctctccattttagatttgttgttttgttactgagacctcttaacaatccatgatcag

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|8284137|gb|BE021696.1|BE021696
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|6454402|gb|AW185085.1|AW185085
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACACTACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|213618065|gb|DB963698.1|DB963698
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACACTACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|12689938|gb|BG156274.1|BG156274
EST:     CAAATTTGGAGAGGAGATGAAGAAGAAATGTACANCTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: CAAATTTGGAGAGGAGATGAAGAAGAAATGTACA-CTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|17022031|gb|BM093065.1|BM093065
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|209709321|gb|BW680986.1|BW680986
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACA
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACA
EST: gi|12690012|gb|BG156348.1|BG156348
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|151394548|gb|EV264419.1|EV264419
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|5606299|gb|AI900405.1|AI900405
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|120531830|gb|EH259963.1|EH259963
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|19936079|gb|BQ080713.1|BQ080713
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
EST: gi|16105072|gb|BI892812.1|BI892812
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATTGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaa ... caaaaatcagGTTAACTATTATGAAATCGACAATACACCTACAGGAACTTGTGCTGTTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagtttaatcttgtgatttgtctcctcctttctttgtgataagctactttgtgcctgacctaagaataccatttctgaaattgactttattcattcaaaaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA