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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

Basic information

species Glycine max
transcript GLYMA06G18530.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
gtaagtttggctctctggatacttttgaggttaatattatc-cagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA
||| |||  | |   || | |  ||||   |  ||  |||| ||      |  |  |   | || ||| ||    |||  |||||| ||||| ||||||||||| |||||||| || |||||||| || ||||||||||||||  |||||||| | |||   || ||| | || || |  ||
gtatgtt--gttgggtgca-atatttggtttgtattctatcacaacaacagcaggatttttgag-ttacgaaag-ctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 7
gtaagtt--tggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA
||| |||  |||  |  ||| | | ||||   |  | |    ||||     |   | | | | | |     || || |   ||||||||| || || || |||||||| ||||| || || |||||||| ||||||||||| || ||||| ||| | ||  | || ||| | ||||| |  ||
gtatgttaatgggaccttggcttcatttggcatgtacaagtaccag-----gggatctgagttacc----aaggttgt---gcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 9
gtaagtt--tggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA--
||| |||  |||  |  ||| | | ||||   |  | |    ||||     |   | | | | | |     || || |   ||||||||| || || || |||||||| ||||| || || |||||||| ||||||||||| || ||||| ||| | ||  | || ||| | ||||| |  ||  
gtatgttaatgggaccttggcttcatttggcatgtacaagtaccag-----gggatctgagttacc----aaggttgt---gcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAGT

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
gtaagtttggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA
    || ||    | ||  |   |||||  ||   ||   | |||        | | | | | |     || ||||   ||||||||| ||  | || |||||||| ||||| || || |||||||| |||||||||||||| ||||| ||| | ||| | || ||||| ||||| |  ||
----gtatgttattgtgccttggtttgattttg-catgtacaagtacagaggatctgagttacc----aaggttct---gcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtttggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatga----gtttctatt------gcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA
||| ||||     |     | |  |  | |||  | |  |   ||     |||     || || ||||||       | ||||       ||||| ||||| ||||||||||||||||| ||| | ||||| || ||||||||||| |||||| | |||||  | || ||||| ||| | |||||||| ||
gtacgtttattaattaaattgcaatgcatgttg-tctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------gtaagtttggctctctgga-tacttttgaggttaatattatccagtttttgttgt--ttaaatcagcttatgagtt-tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA
             |  | | | ||| | |  | |||   ||| | ||    ||    | |     |||  || ||| |  ||||   || | | ||  ||||||| ||  |||||||||||||||| || || |||||| |||| ||||||||| ||||  | ||||| || ||    || ||| ||| ||| |  ||
tccctcgaagaaggctactgtagctgtatctactacacatgacggtagccgtacatggatcaatatgtcttttaataactttattcattgtttgttttagGGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGA

upper sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------gtaagtttggctctctggatacttttgaggttaatatt--atccagtttttgttgtttaaatcagcttatgagttt-ctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA
                                                                                             ||  || | | ||    |  ||     |   || ||  | ||| | |   |  |||  |   | |   |  ||| |||| ||||||||| || |||||||||||||| || ||||| |||||| |||| ||||||||  | ||  | |||||||| ||    || ||| | ||||| |  ||
gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttgctatggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGA

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|10846474|gb|BF069349.1|BF069349
EST:     ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
EST: gi|208025821|gb|GD826655.1|GD826655
EST:     GGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
genomic: GGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
EST: gi|7925599|gb|AW831625.1|AW831625
EST:     ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATTTGGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
EST: gi|192330548|gb|FK021251.1|FK021251
EST:     ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
EST: gi|193389612|gb|FK357199.1|FK357199
EST:     ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCCTGGCCATGAT
genomic: ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATC-TGGCCATGAT
EST: gi|31307855|gb|CD393058.1|CD393058
EST:     ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
EST: gi|15201058|gb|BI424670.1|BI424670
EST:     ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTT
genomic: ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTT
EST: gi|10232123|gb|BE801011.1|BE801011
EST:     ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT                         GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATG
EST: gi|214004373|gb|DB985041.1|DB985041
EST:     ATGTGATATATGGAGTGTGGG-AGCTATACTGGTTGAATTATGCACT                         GGTGAAGC-TTATAGGCTGACTCATGAAAATTTAGAGCATCTGGCCATGAT
genomic: ATGTGATATATGGAGTGTGGGTTG-TATACTGGTTGAATTATGCACTgtaagtttgg ... tctattgcagGGTGAAGCTTTGT-TTCAGACTCATGAAAATTTAGAGCATCTGGCCATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA
 ggttaat  putative branch site (score: 4)
                                           tttctatt  putative PPT
                tttttgttgtttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA