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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcctaaaatatatttttcttattcatttatcctcaaatagttgtttagttatgagctctcatctcttcgtttccttccttgtctctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACTTTCCTTTTCATTATTAGAAGTTCCAATACAGATGCCAACAAAACAAGAA

Basic information

species Glycine max
transcript GLYMA20G31840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31840.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0012g01580.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------gtactgcctaaaatatattt-----ttcttattcatttatcctcaaatagttgtttagttatgagctctcatctcttcgtttcc---------------------ttccttgtctctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACTTTCCTTTTCATTATTAGAAGTTCCAATACAGATGCCAACAAAACAAGAA
                                   || | | | ||| || ||         ||    |||  || |   | | |  |||  || | || |    ||||||   ||                       |  ||  ||   | || |||||||||||||||||||| || || |||||| |||||||| |||| |||||  | |||||||| ||||| | |||||     |||   |      ||    
gtaccctttcagtgaccttgaatttatataagttctatttcttgaaaaatgttaaaacacgtttccctattcctcatgggagattattttctttgtaagtttggttctctttaattatagtgttattgaaattgatggttctctaatcctaaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACCCTTCTTTTCATAATTAGGACTTCCAGCCACGATTTGAGATCCTCATCTT
















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|298187634|gb|HO034783.1|HO034783
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGA
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGA
EST: gi|193693275|gb|FK627230.1|FK627230
EST:     ATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: ATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|58016676|gb|CX703418.1|CX703418
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|193707908|gb|FK647704.1|FK647704
EST:     ATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: ATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|58020292|gb|CX707034.1|CX707034
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|16996305|gb|BM085677.1|BM085677
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|208050722|gb|GD848577.1|GD848577
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|13787967|gb|BG650559.1|BG650559
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|193714075|gb|FK650553.1|FK650553
EST:     ATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: ATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
EST: gi|298193968|gb|HO040616.1|HO040616
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTCCAATCACAGTCCTGCCATG                         AATGCTACTGGA
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGA
EST: gi|192329380|gb|FK021834.1|FK021834
EST:     TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATG                         AATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT
genomic: TTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgccta ... ctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtttagttatgagctctcatctcttcgtttccttccttgtctctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACTTTCCTTTTCATTATTAGAAGTTCCAATACAGATGCCAACAAAACAAGAA
                ctctcatctcttcgtt  CT-rich tract
     ttagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcctaaaatatatttttcttattcatttatcctcaaatagttgtttagttatgagctctcatctcttcgtttccttccttgtctctatttccagAATGCTGCTGGAGGAATTCTGGGGTTGGTTGGTGCCATGTTTGTGGAAACTTTCCTTTTCATTATTAGAAGTTCCAATACAGATGCCAACAAAACAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG