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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctctaatttgcttgccatcatgtttatatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata...

Basic information

species Glycine max
transcript GLYMA16G01830.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os04g47970.1 (Oryza sativa), 5'ss of exon 2
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttc---tctaatttgcttgccatcatgtttatatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgtta-tata
|||| ||||| || |||||||||||||||||||||||  | |||||||| |||||||||||||| ||||| || ||||| || || ||||||||||| |||||||      |||  |  | |||   |    |||   ||||    |       |  | |||||  || |  ||||   | |   ||      |   || || |
ACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGAAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataaatctgttgcgattgattttccttttcactacagcattgaaaatatg-gatgatg--attgattctacata-gccagtaagtagtaactagtaaa

upper sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 5'ss of exon 2
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagt--tctctaatt--tgcttgccatcatgttta--tatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata
|||| || || ||||| | ||||||||||||||||||  | |||||||| || ||||||||||| ||||||||||| ||    || |||||| | || ||||||||  |||   |||  | |||  ||||   || |  ||||||||  |||  ||      | | |   ||||  | || |  |          ||         
ACCAGGGAATGTACAACACATTGACTTGGTGGGAGCAAATGGACAATGGCAAACAGCTTACTCGCAACAGGAAGTTCCTTGTTGTAGTTCCTGTTGTCCTgtaagtattcttctattacttcttagcatccatttcaattatacaaacttattggcgggcacttaggatttaggagcaataacaggcaacatgtactcaa------

upper sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G064898_T02 (Zea mays), 5'ss of exon 2
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttc--tctaatttgcttgccat-catgtttatatacaaaggtatct-gcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata
||||||| |||||||  |||||||| |||||||||||  | ||||||||  ||||||||||||| |||||||||||| | || || || ||| |||||||||||||||  ||| ||   |||||  | ||    |  | | |    | | | | ||||||  | |  ||      ||  |||  ||     |  | ||| | | 
ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttccatctcatcctcttgcagttcacacatgaacaaattactctttagattctggaaaggaaattaa---tactaatcagtacaggcagtggttgttt-

upper sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G044720_T02 (Zea mays), 5'ss of exon 1
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctctaatttgcttgccatcatgtttatatacaaaggtatctgcttctggtgatgtcataggg---tctatgaatgtgtgtgcacccttgttatata--
||||||| |||||||  |||||||| |||||||||||  | ||||||||  ||||||||||||| ||||| |||||| | || || || ||| |||||||||||||||    || |  |   |||   ||| | | |  ||  |     |||  |||  ||  |  |     | ||  |||  ||     |  |  ||   |   
ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcc---atctcatcctcatgcagttcacacatcaaattgct--ctttaggttctgcaaaggaaatttatactaatcagttcaggcagtatttgcttgtg

upper sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G114911_T02 (Zea mays), 5'ss of exon 2
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttct--ctaatttgcttgccatcatgtttatatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata--
|||| || || |||||   ||||||||||||||||||  | || ||||| || |||||||||||||| |||||||| ||||  ||||||||| | || |||||||| ||  | |   |   |    |||  || || | ||    | | ||  | || | | |  | |   | | |||   |   | ||| |    | | |   
ACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctgcccatcgtatctctgttcaatttcattttcattc-tctatggctatgtttaggagaaatattatgtga---tagatacactcaaaatgtttgct

upper sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 2
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttct--ctaatttgcttg-ccatcatgtttatatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata
|||| || || ||||| | ||||||||||||||| ||  | |||||||| || |||||||||||||| |||||||| ||||  ||||||||| | || |||||||| ||  |   | |  ||  || ||   |||   |  ||   | | ||  | || | | |  | |   | |||||   |    |||| |    | | | 
ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctggccgttatatttctccgtccaatttcattttaattctctatggctatgtttaggaaaaatattatatga---tagaagcactcaaaatgtttg

upper sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G558324_T01 (Zea mays), 5'ss of exon 3
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttct--ctaatttgcttgccatcatgtttatatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata--
|||| || || |||||   ||||||||||||||| ||  | || ||||| || |||||||||||||| |||||||| ||||  ||||||| | | || |||||||| ||  | |   |   |    |||  || || | ||    | | ||  | || | | |  | |   | | |||   |   | ||| |    | | |   
ACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCATGTTGTCCTgtaagtgctgcccatcgtatctctgttcaatttcattttcattc-tctatggctatgtttaggagaaatattatgtga---tagatacactcaaaatgtttgct

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|208335534|gb|GE137553.1|GE137553
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|31459292|gb|CD401320.1|CD401320
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|254346297|gb|GR859910.1|GR859910
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|298185731|gb|HO030944.1|HO030944
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTT
EST: gi|208255918|gb|GE053611.1|GE053611
EST:     TTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: TTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|254348679|gb|GR852358.1|GR852358
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACA-CAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|16348288|gb|BI973883.1|BI973883
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACA
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACA
EST: gi|15284804|gb|BI468695.1|BI468695
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|151412762|gb|EV282574.1|EV282574
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|193566659|gb|FK525992.1|FK525992
EST:     AAGCAGCATACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|5606135|gb|AI900233.1|AI900233
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGCTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|254346298|gb|GR859911.1|GR859911
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATT
EST: gi|16996257|gb|BM085629.1|BM085629
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCT                         GTACTTGATAGCCTCACACACAA
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAA
EST: gi|21601782|gb|BQ612113.1|BQ612113
EST:     AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGGGCT                         GTACTTGATAGCCTCACACCCAACAGACTATCAGAATCCAATGTTCTTA
genomic: AAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctc ... tgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctctaatttgcttgccatcatgtttatatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT