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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttactggttctctcattctgcatggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

Basic information

species Glycine max
transcript GLYMA01G07070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttactggttctctcattctgcatggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaactt--acagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
||||   |   ||| ||       |||| || |  || ||   ||||    | | | | | | |||| | | |  | ||||||||  |||||||||||||||||||||||||||||||||||||||||||||| || ||||||||| |||| || ||||||||||||||||||||| |||| |||||||||
gtaatgcatatgtt-tcaagcatagcataga-ctgttcaagccttttaaaagattgttatggcctga-tttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG

upper sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagttactggttctctcattctgcatggatcc---atttaattgtttttgttgctagctcttgtctgaatatc--att-actgaa-acttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
||||| |  ||  | |    || || |||  |     |  |  || | |||       | || |  |||| | |   ||| ||||     |   ||||| ||||||||||| |||||||| || || ||||||||||| || ||||||||  ||||||| ||||| |||||||||||||| ||||||||||| || 
gtaagattttgagt-tgaggttttggatgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGACACATTGAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAACTA

upper sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------gtaagttactggttctctcattctgcatggatccatttaatt-gtttttgtt---gctagctcttgtctgaat---atcattactgaaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                                                                  |  | || ||     | | | |          | |||| ||  || |    | | || |  ||   |||    |  |       | ||||||||| ||||||||||| |||||||| ||||||||||| || || ||| |||| ||  ||||||||||||| |||||||||||||| |||||||||||| ||
gtaagattgtggtagttgattatgcggtgaagcagatgagagtgattgaaccgtctattggacggggccattgattgatgaagttttcggtagcatgctgaatttgtgcttatctgggtttgcaccggtaataatcaggtagtggtatggaattacagGGCATGCCATTTGGCGAAGCAAGCATTTGATGAGGCTATCGCTGAGCTGGATACGTTGAGTGAAGAGTCGTACAAGGACAGCACATTGATCATGCAGTTG

upper sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------gtaagttactggttc-tctcattctgcatggatccattta---attgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                        | || |  |||||  | | |    |  |   |   || |   ||||  | | |||  ||||  || ||||||  ||||   ||   |  |||||| ||||||||||| || ||||| ||||| ||||| ||||| |||||||| ||  | ||||| ||||| |||||||||||||| |||||||||||||| 
gtatgaattttggtcagtagagacttagctgttggttggttttacggcgtgttttttttttcagggattgaatatattgg-agcttgtgactgaatgccatt---gactgtggcagGGCATGCCATTTGGCGAAACAAGCATTTGACGAGGCGATTGCTGAGTTGGATACGTTAAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAGCTA

upper sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S348_15V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------gtaagttactggttctctcattctgcatggatccatttaattgtttttgttgctagctcttgt-ctgaatatcattactgaaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                                                                                   ||   |  |  ||         |    ||||| |||    ||||  | ||    |   ||    | |  | |  |      |  || ||| || ||||||||||| |||||||| ||||||||||| || |||||| |||| ||  |||| || ||||| |||||||||||||| |||||||||||||| 
gtaagagtggctgtgtggcatgcggcgaagcggttgagggtgattgtggaggcgtggatggaacgtgggcgtgggatggatgggtggatagcatgtgtgtgggggcgtggtggattcat--ggttgtggtggtccgcaatgctgaaacggggtgtggtggtgtgagatttcagAGCATGCCATTTGGCGAAGCAAGCGTTTGATGAGGCGATCGCGGAGCTGGATACGTTGAGCGAGGAGTCGTACAAGGACAGCACGTTGATCATGCAGCTA

upper sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36243 (Selaginella moellendorffii), 3'ss of exon 4
--gtaagttactggttctctcattctgcatggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
  |  ||   || || ||||  ||  |  |    |  || || ||  ||||| |||     ||||       ||  |  || |||    || || |||||  | || |||||||||||||| || || || |||||| ||||||| || || ||||| || ||||||||||||||||||||||||||||| 
gtgagagcgcctcgtcctctt-tttagttttctccacttcaactgactttgtggct-----ttgtt------tcgctgttgcaac----agCGCTTGCCAGCTAGCCAAGCAAGCTTTTGACGATGCGATCGCGGAGCTGGACACGCTCAGCGAAGAATCCTACAAGGACAGCACTTTGATCATGCAGCTT

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|21638509|gb|BM139555.1|BM139555
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|18735212|gb|BM528632.1|BM528632
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|192303428|gb|FG997458.1|FG997458
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|192300602|gb|FG988899.1|FG988899
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|12773324|gb|BG238251.1|BG238251
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|7590427|gb|AW706180.1|AW706180
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|58019744|gb|CX706486.1|CX706486
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|58019157|gb|CX705899.1|CX705899
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|21889266|gb|BQ742479.1|BQ742479
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|214004600|gb|DB988970.1|DB988970
EST:     TTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: TTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|12773840|gb|BG238767.1|BG238767
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|58015355|gb|CX702097.1|CX702097
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|58019309|gb|CX706051.1|CX706051
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|58022129|gb|CX708870.1|CX708870
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|192302132|gb|FG995812.1|FG995812
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|18735497|gb|BM528797.1|BM528797
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGANGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|26057311|gb|CA800225.1|CA800225
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|58018950|gb|CX705692.1|CX705692
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttact ... aaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
 atttaat  putative branch site (score: 4)
                                aatatcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttactggttctctcattctgcatggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG