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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaggacagaaattttattcggtttgcgtgttaatattgtcatccttacattgcatattgggaaatcttttggcaaataaacttattatatggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG

Basic information

species Glycine max
transcript GLYMA10G44190.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G33230.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gggaggacagaaattttattcggtttgcgtgttaatattgtcatccttacattgcatattgg--gaaatcttttggcaaataaacttattatatggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
| || |||| || | | ||||| | ||||| || | | || ||| || || ||| ||| || ||||||| | |||||||| |||| ||| |||| ||| |||| || |||||||||||||| || ||||| |||||| |||| | | ||||||
aggccttagtgggttgatgatttggatctgaagttatcttaatgtatatatcctctcaatcgaagatgactaaaacctcttcattgatatgctt---------ttgcagGTGGCTTTATCATCATTATTTTGCAATGGCTATGTCCCTTGTCAGTCTCACTTGGGAAATCAAAGGTCAACCAAACTGCGTTCAGAAGCAG

upper sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 3'ss of exon 5
gggaggacagaaattttattcggtttgcgtgttaatattgtcatcc--ttacatt-gcatattgggaaatcttttggcaaataaacttattatatggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
|||| ||| | || | |||| || |||| | || ||| | || | | || || |||| || | || || | |||||||||||| |||||||||||||||||| | ||||| ||||| |||||||| ||||| || || ||||||||| |||| ||| ||||||||
-aactgacaacaatatgatactgtttaaactttcatatatttggttagttttattagtatcatctgtcatagctta-caaaaaatcccat-atgctttcgcagGTGGATATACCATCACTATTGTGCTATGATTATGGCTCTCGTTAGTCTCACATGGGAAATCAAGGGACAACCAAACTGCGCACAAAAGCAG

upper sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S359_2V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------gggaggacagaaatt---ttattcggtttgcgtgttaatattgtcatcct--tacattgc----atattgggaaatcttttggcaaata-----aacttattatatggtta---cagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
|| || | || || || || | ||| || ||| | |||| | | || | | || ||||| ||| | | || || | | ||||||| | |||||||| |||||||| ||||||||||| || |||||||| || |||| | || || || || |||
gtacttttcttcactgaaccttccaacgatggttttcgttaagtttattcgttttgttggaggaagttccatcatcagcttttttggacggtccattatcatgcaggccctaatgcatttccatcaatttcgcgattcgtttggattatagtgggagaatgttgcattgatgtggcagGTGGGTGTATCATCATTATTGTGCAATGGTGATGGCACTGGTGAGTCTTACATGGG---------GTCATCCTAGTTGCATTCGCAAACAG

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|58021387|gb|CX708128.1|CX708128
EST:     GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG                         GTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC
genomic: GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTGgtatagtcat ... atggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC
EST: gi|58024474|gb|CX711215.1|CX711215
EST:     GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG                         GTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC
genomic: GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTGgtatagtcat ... atggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC
EST: gi|23727946|gb|BU762014.1|BU762014
EST:     GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG                         GTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC
genomic: GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTGgtatagtcat ... atggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC
EST: gi|254346987|gb|GR857191.1|GR857191
EST:     GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTG                         GTGGATATACCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC
genomic: GCATTGCGAGAGAACATATTGAGAGTCAATGGAAGTGATATTCGTCCCTGgtatagtcat ... atggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacattgcatattgggaaatcttttggcaaataaacttattatatggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
 tccttac  putative branch site (score: 2)
 aaataaacttattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggaggacagaaattttattcggtttgcgtgttaatattgtcatccttacattgcatattgggaaatcttttggcaaataaacttattatatggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT