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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttgtttcacccatttttcactatttctttctcttgtcaggtctttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG

Basic information

species Glycine max
transcript GLYMA18G02210.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 7
--gtatatttgtttcacccatttttcactatttctttctctt---------gtcaggtctttgattctatctgctttgt---tgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
   |  | ||  | ||   ||| |||   |    | |  | |              || || ||||  | ||  |   |   | | | ||||||||||||| || || || || |||||||| || ||||| |||||||| |||||||| |||||||| || |||| |||||| ||| |||||||||| ||||
gtttgcaatttgtccatggattcttctgcagcagtatgccattaaaaaaaaacttagttttggattaaaacttgtccatgtattcttctgcagTATGTGCCGTATGTTGGAGACAGCAAGAGGGCAATGGACGAGTACACCTCAGAGATCTTCATGGGGGGTAAGAGCACCATCGTTCTGCACAACACCTGTG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 7
----------------------gtatatttgtttcacccatttttcactatttctttctcttgtcaggtctttgattctatctgct--ttgttgcct-ttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                      | | | || |  | | | |  | |||  |  ||     |  |  |||   || ||||||    |  |||||   | ||||||||| | || ||||| ||||| |||||||| |||||||| |||||||| || ||||| |||||||| || ||||||||||| ||  |||||||||| || |
ctccgatagaatctgccagaccgaaaaattataccccgc-tgatgcacggtggctga---tgatttggttgctgtttctattgagtaattgttaattgttgcagTATATTCCATACGTTGGGGACAGCAAGAGGGCCATGGACGAGTACACCTCGGAGATCTTCATGGGAGGGAAGAACACCATCGTGCTGCACAACACCTGCG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 7
----gtatatttgtttcacccatttttcactattt-ctttctcttgtcaggtctttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
    ||    |  | |  | | |  || |   ||  | |   |  | ||| | |    |   |  ||      |    |||||||||||||| ||||| || || |||||||| || ||||| |||||||| |||||||| |||||||| || ||||||||||| ||  |||||||||| ||||
gtctgttagctgatctttcacctcgttaaaagttgacatatgcaaggcagatttacattgaaacttgtcactcttttgttgcagTATGTGCCGTACGTGGGAGACAGCAAGAGGGCTATGGACGAGTACACCTCAGAGATCTTCATGGGCGGCAAGAACACCATCGTGCTGCACAACACCTGTG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 5
gtatatttgtt--tcacccatttttc------actatttctttctcttgtcaggtctttgatt----------ctatctgctttgttgcctt-tgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
|| |||| | |  ||  |||  | |        ||    | | |    ||     | | ||||          ||  |  ||   ||||    ||||||||||||| ||||| || || || ||||| || ||||| |||||||| |||||||| ||||||||||| ||||||||||| ||  |||||||||| ||||
gtctattagctaatcttccacctctttaaaaagctggcacatgcagcagtttaaacgtagatttacattaaaacttgccactcctttgctgcatgcagTATGTGCCGTACGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGTGGCAAGAACACCATCGTGCTGCACAACACCTGTG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 3
---------------gtatatttgtttcacccatttttcactatttctttctcttgtcaggtct---ttgattctatctgctttgttgcctt-tgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                |  |  | ||| |     |      |    |  | |      || | |   ||||  ||  |  ||   |||     ||||||||||||| ||||| || ||||| ||||| || ||||| |||||||| |||||||| || |||||  | |||||||||||  |  |||||||||| || |
gtctgttagctgaacttccacctctttaaaaagatggcacatgcagcagtttaaacgtagatttacattgaaacttgccactcatttgttgcatgcagTATGTGCCGTACGTGGGAGATAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTTATGGGCAGCAAGAACACCATCATGCTGCACAACACCTGCG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 7
gtatatttgtt--tcacccatttttcactatttctttctcttgt-------------caggtct---ttgattctatctgctttgttgcctt-tgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
|| | || | |  ||  |||  | |    |   ||  | | ||               || | |   ||||  |   |  ||   ||||    ||||||||||||| || || || || || ||||| || ||||| |||||||| |||||||| |||||||| || |||| |||||| ||  |||||||||| || |
gtctgttagctgatcttccacctctttaaaaagctggcacgtgcagcagtttaaacgtagatttacattgaaacctgccactcctttgctgcatgcagTATGTGCCGTATGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGCGGCAAGAGCACCATCGTGCTGCACAACACCTGCG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G177461_T01 (Zea mays), 3'ss of exon 7
----------------------------gtatatttgtttcacccatttttcactatttctttctcttgtcaggtctttgattctatctgctttgt-tgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                            ||   |  || |  ||||| | |  ||| ||| |  |  ||     |  ||  |   |  || |   | | | |||||||||  | || || || || || ||||||||||||||||| || || || || ||||| |||||||| || ||||||||||| ||  |||||||||| ||||
gtcggtcggtccacttgttgtttagtttgtgactgagtctatcccatatat-gctacttcatgtt--tgattaattgttactcaaagttgatccctcttcttttgcagTACATCCCCTATGTGGGTGACAGCAAGAGAGCCATGGACGAATATACCTCCGAGATCTTCATGGGCGGCAAGAACACCATCGTGCTGCACAACACCTGTG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G010768_T01 (Zea mays), 3'ss of exon 1
---------------gtatatttgtttcacccatttttcactatttctttctcttgtcaggtct---ttgattctatctgctttgttgcctt-tgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                |  |  | ||| |     ||     |       | |      || | |   ||||  ||  |  ||   |||     ||||||||||||  ||||| || || || ||||| || ||||| |||||||| |||||||| ||||||||  | ||||||||||| ||  | |||||||| | ||
atttgttagctgatcttccacctctttaaaaagcttgcaggtgcagtagtttaaacgtagatttacattgaaacttgccactcatttgttgcatgcagTATGTGCTGTACGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGCAGCAAGAACACCATCGTGCTACACAACACCTATG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G071174_T01 (Zea mays), 3'ss of exon 2
----------gtatatttgtttcacccatttttcactatttctttctcttgtcaggtctttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
            | | | | |       ||| | |||  | ||   |||||        |||||   |||  |  | |    |||||||||  | || ||||| || || |||||||| || ||||| ||||| || || ||||| ||||||||||| ||||||||||| |   |||||||||| || |
gtgggtcggtcgacactagctagttgtgtttgtgactgatgctgcttcttgctcaaaggttgatga-atcatccctata--ttttgcagTACATCCCCTACGTGGGTGACAGCAAGAGGGCTATGGACGAGTATACCTCTGAGATCTTCATGGGTGGCAAGAACACCATCGCGCTGCACAACACCTGCG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatatttgtttcacccatttttcactatttctttctcttgtcaggt-ctttgattctatctgctttgttgcct----ttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
   |  ||  ||   | |||  | |  |||      |||    |    | || |    |  |    | |||  |    |||||||||||||| |  ||||| || ||||||||||| |||||||| ||||| ||||||||||||||||| || |||||||| |||||  |||||||||| ||||
--gtgattaattttactattaattataattatccaatctaacaaatcacattaacataaattatactattggatggtgttgcagTATGTGCCATGTGTAGGAGACAGCAAGAGAGCAATGGATGAATACACATCAGAGATATTCATGGGAGGGAAGAACACGATTGTGATGCACAACACTTGTG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------gtatatttgtttcacccatttttcactatttctt---tctcttgtcaggtctttgattctatc--tgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                 |     |  | | | |||  ||  |  || ||   |   || | | |||||  || ||     || | ||     ||||||||||||||| || || | |||||| || ||||| |||||||||||||| || |||||||||||||| || | |||||| || || ||||| ||||| ||||
gtttgattttgaatcagaggccagagtgatcaattcctcctttctttttaagtacattttaaagtcttaaatcctgctattgttctgaatgttttgcagTATGTGCCATATGTTGCGGATAGTAAAAGAGCAATGGATGAGTACACGTCTGAGATATTCATGGGAGGGAGGAACACTATAGTGTTGCATAACACTTGTG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
--gtatatttgtttcacccatttttcactatttctttctcttgtca------ggtct--ttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
    |||          |      |||  |  | ||||| ||| ||      | ||   ||||| | || || | ||||   |||| ||||||| || || || | |||||| ||| |||||||||| |||||||| ||||||||||||||||| || |||||||| |||||  ||||||| || || |
gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttg-tgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------gtatatttgtttcacccatttttcactattt----ctttctcttgtcaggtctttgattctatctgct-ttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                       || | | ||| | ||   |      ||  ||    ||   || |      |   | |   |||  | | ||||||   |||||||||||||| || || || |||||||||||||||||||||||||||||||| ||||||||||||||||| |||| |||||||||  |||||||||| || |
gtatatcgcagaaccctccttttgtttgtatgtattacaattcagatgctggtttggactcattcattctcactggctaacattatacggtgttgttgatattgcagTATGTGCCATATGTTGGAGATAGCAAGAGAGCCATGGATGAGTACACTTCTGAGATATTCATGGGTGGGAAGAGCACCATTGTGCTGCACAACACCTGCG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------gtatatttgtttcacccatttttcactatttctttctcttgtcaggtctttgattctatctgctttgttgcc----tttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                                                      |  ||||    | || | || ||   |||     |  || ||   ||||    |  | |    |   || |    | ||||||| || ||||| || || || |||||||| || ||||| ||||||||||| ||||| |||||||| |||   ||||| || ||  ||||||| || || |
gtattcttatctctactccagccctgcagtcaatgttttcaagccatttcggctttgatttcagactccaagttgtctgcattcacaccgattctcgaatcttcctcttaaccaaaatcaatgacggcgtctgcagTACGTCCCTTATGTGGGTGACAGCAAGAGGGCAATGGACGAGTACACTTCGGAGATCTTCATGGGCGGACGTAACACAATCGTCATGCACAATACGTGCG

upper sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 7
gtatatttgtttcacccatttttcactatttctttctcttgtcaggtctttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
        ||   ||  |   ||    |||| |||||   |  |  ||     ||     ||||||  |   |||  ||||||| |||||||| || ||||||||| | |||||||| || ||||| || |||||||||||||| || | || |||||| |   |||||||||| || |
--------gtaaaacaaacgcttg---atttttttctagggaaaactcccgagtt-----tgctttcgt---tttctagTATGTTCCTTACGTCGGTGATAGCAAGCGGGCCATGGACGAATACACGTCCGAGATATTCATGGGAGGCAGGAGCACCATCGCCATGCACAACACTTGCG

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|19453629|gb|BM955039.1|BM955039
EST:     CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAG                         TATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
genomic: CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAGgtatatttgt ... gcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
EST: gi|208071333|gb|GD872192.1|GD872192
EST:     CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAG                         TATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
genomic: CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAGgtatatttgt ... gcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
EST: gi|11688361|gb|BF596037.1|BF596037
EST:     CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAG                         TATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
genomic: CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAGgtatatttgt ... gcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
EST: gi|13788721|gb|BG651312.1|BG651312
EST:     CCATCCTCTATGAGCCTGGTGAACATCCAGACCATGTTGTTGTTATTAAG                         TATGTGCCTTACGTAGGGGACAGCAAGAGAGCCATGGATGAGTACACTTCA
genomic: CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAGgtatatttgt ... gcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
EST: gi|13790045|gb|BG652636.1|BG652636
EST:     CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAG                         TATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA
genomic: CCATCCTCTATGAGCCTGGTGAACATCCCGACCATGTTGTTGTTATTAAGgtatatttgt ... gcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatttctttctcttgtcaggtctttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG
                       ctttgat  putative branch site (score: 5)
                                           ttgccttt  putative PPT
                        tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttgtttcacccatttttcactatttctttctcttgtcaggtctttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC