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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtaaagaattttagtaatgttttatggatgctgtcaacatttgtcgttgacatgatgctgatgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA

Basic information

species Glycine max
transcript GLYMA10G30020.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
gtaagt-tgtaaagaattttagtaatgttttatggatgctgtcaacatttgtcgtt-gacatgatgctgatgtatctacatc-tgttg-cagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
||  |  | |       |  ||||      | || ||   ||     ||| | ||| ||  | || ||  | | | |   |  | ||| |||||     || |||| ||||||||||| |||||||| ||||||||||| ||||| ||||| || ||||||||||| || |||||||||||| | || || |
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttat-ctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 7
---------------------------gtaagttgtaaagaattttagtaatgttttatggatgctgtcaacatttgtcgttgacatgatgctgatgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
                            ||  |  |  ||| ||| || |||||    |  ||    | ||   |  | | | |  ||||  | |  | | |   | ||| ||||||   | || ||||||| ||||| || || ||||| ||||||||||| ||||| || |||||||||||||| || || |||||||| ||  |||| ||||
gtaagcaccctgtactattagcatcatatagatcctgcaga-tttgagcaatgtcagctaaat----ttaattgtaatggataatctgatattaacctgtttctttttgtggcagTTGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 9
---gtaagttgtaaagaattttag-taatgttttatggatgctgtc---aacatttgtcgttgacatgatgctga-----tgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
   | |   |||||    ||| |  | |  ||  |         ||   |  |  ||   |||| ||  |  |       |  || || || | || ||| |     |||||||||||||||||||||| ||||| | ||| || || ||||| ||||| || |||||||| ||||| || || || || || |||||||
ttggcagtctgtaatttctttaatctcactttgcaccagcatcttccaaagtacatgatattgatattttttttgaccctttcatatatatatatttcagCTGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 6
gta-agttgtaaagaattttagtaatg--ttttatggatgctgtcaacatttgtcgttgacatgatgctgat-gtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
||  |  | | |  |  | | | || |   || | |  || ||||    ||  ||  | |  |||  ||| |  ||| ||   |  |||||| |     |||||||||||||||| || |||||||| || || || || ||||| ||||| |||||||| || ||||| ||||| |||||| |||| ||||
gtgcacctctgatcagatgtggcaagggaattcacgcttgttgtc----ttactctcttaactgactctgttcatatatatggcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G311165_T01 (Zea mays), 3'ss of exon 8
----gtaagttgtaa---agaattttagtaatgttttatggatgctgtcaacatttgtcgttg--acatgatgctgatgtatc-tacatctgttgca-gTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
    | |   ||||      |  | |    |  ||||     |  |   | ||    | | ||  |  || |  | | |  |      | | ||| | |||     || ||||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| || || || || ||||| ||  |||| ||||
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagTTGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
----gtaagttgtaa---agaattttagtaatgttttatggatgctgtcaacatttgtcgttg--acatgatgctgatgtatc-tacatctgttgca-gTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA-
    | |   ||||      |  | |    |  ||||     |  |   | ||    | | ||  |  || |  | | |  |      | | ||| | |||     || ||||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| || || || || ||||| ||  |||| |||| 
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------gtaagttg---taaagaattttagtaatgtttta---tggatgctgtcaacatttgtcgttgacatgatgctgatgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
                                            ||   |||   |  ||  || || | |  ||  |   | |||      | |||||   ||        || |  |   | |   | |  ||||| |||  ||| |||||||||||||||| ||||| || ||||| ||||| ||||| ||||| || ||||| || || || |||||||||||| |||||||||
gtaagatttcttttaacttcttgggcacttccctggcccctgttgtctattggcattgagtgttctatttagattcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggttgtcctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------gtaagttgta----aagaattttagtaatgttttatggatgctgtcaaca--tttgtcgttgacatgatgc----------tgatgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
                                                                          | | || ||    |  |   ||  | |  |||  | | || |||| |    ||| |      || ||||           || | | | |  ||    ||||| | |  || |||||||| ||||| || || ||||||||||| ||||| ||||| || || |||||||||||||| || || || ||| || | |||||||
gtcccccttcctctctctctctctcgactatatgcattgtttggattaaagagtctattagtttctttttaatttcaattctatttcagcagcgttgttgaaatttagtcgctgatgtctattattttattccctgcacgatgaactcatttcgtgttttctgtgtattgcatgcagCTTTTCTACCTGAGTGGAATTCTTACCGTCTTCTTTTGTGGCATTGTAATGTCACACTACACCTGGCATAACGTCACTGAAAGCTCACGAGTAACTACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------------------gtaagttgtaaagaattttagtaatgttttatggatgctgtcaa--catttgtcgttgacatgatgctgatgtat-ctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
                                                                      ||       | || |  |||    ||| || |   ||| ||  ||   ||  | || ||  | ||   |||| |    | | |||||| | |  ||  ||||||| |||||| | || |||||||| || ||||| ||||||||||| || ||||||||||| || |||| |||  ||||||| | ||
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------------gtaagttgtaaagaattttagtaatgttttatggatgctgtcaacatttgtc------gttgacatgatgctgatgtatc-tacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
                                                                                    | | ||| |   |  ||      |  ||   | |   |||  |   || ||       |  ||   |||||  | | || |  ||    ||||| | |  ||  ||||||| ||||| ||||| ||||||||||| ||||| ||||| || |||||||||||||| || || || || ||  |||| || ||||
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttgtaaagaattttagtaatgttttatggatgctgtcaacatttgtcgttgacatgatgctgatgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
               |  ||||  | || | |  |    |  | ||||| |  |||   | ||||  |||         |  || ||| | |  || |||||||| || ||||| || ||||||||||| ||||||||||| |||||||| ||||| ||||| || ||||| ||||||||||| ||||
--------------gtgatagtttttttctgtatagagaggtagcatttcttcttgttctcatgcgtatg---------ccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

upper sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttgtaaagaattttagtaatgttttatggatgctgtcaacatttgtcgttgacatgatgctgatgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
               |   |||  | || | |  |    |  | ||||| |  |||   | ||||  |||         |  || ||| | |  || |||||||| || ||||| || ||||||||||| ||||||||||| |||||||| ||||| ||||| || ||||| ||||||||||| ||||
--------------gtgagagtttttttctgtatagagaggtagcatttcttcttgttctcatgcgtatg---------ccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

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|21601836|gb|BQ612167.1|BQ612167
EST:     AGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA                         TTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATG
genomic: AGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAAgtaagttgta ... tctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATG
EST: gi|254323350|gb|GR835851.1|GR835851
EST:     AGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA                         TTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGG
genomic: AGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAAgtaagttgta ... tctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgctgtcaacatttgtcgttgacatgatgctgatgtatctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
                             tgctgat  putative branch site (score: 3)
         aacattt  TA-rich tract