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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacagtactcacagttgttgatgatattatttgtcatttttatttgtaattttcgtttgaactcattttgcctggctgtgtag

Basic information

species Glycine max
transcript GLYMA03G06440.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G06440.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0004g07150.t01 (Vitis vinifera), 5'ss of exon 2
GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacagtactcacagttgttgatgatattatttgtcatttttatttgtaattttcgtttgaactcattttgcctggctgtgtag---------------
||  ||||||| |||||||| ||||||||||| ||||| ||||| || |||||||||||||| ||||| || || |||||| ||      ||       ||   || |   |||  | | |  | || | |   |  | ||  |||   ||||| |   ||| |                 
GCACGAGGGTTAAAGAAACATTTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgataagcttttctcagt--gtgtttccattacttaataatgttag-accctcgggttttacttgctttgctttaatgtcttataatctgtcatacag

upper sequence: GLYMA03G06440.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S2_16V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacagta-ctcacagttgttgatgatatt-atttgtcatttttatttgtaattttcgtttgaactcat---tttgcctggctgtgtag-------
||  | || |||||||| || ||||||||||||||||| || |  |||||||||||||||||| | ||||| ||||||||| ||     | ||  |  || |     |  || | | |||||  |  |  | | || ||     | ||||    || |  || | || |         
GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAGGCACTGGATGCTTGACAAGTTGGGTGGTGCCTTTgtaagttttacatcttgcttttatactcaacgttcaatcgtcatgctagtacgcatttctctgactatctcagggattcgaatgtcagtctcagcgaatt

upper sequence: GLYMA03G06440.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S81_172V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacagtactcacagttgttgatgatattatttgtcatttttatttgtaatttt--cgtttgaactcattttgcctggctgtgtag----------
||  | || |||||||| || ||||||||||||||||| || || || |||||||| |||||  | ||||| ||||||||  || |  |               || | ||  | |     || || ||||||     ||       |   |    ||| |    |||          
GCTCGTGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAATTGGGTGGCGCCTTTgtgagttcttttactttgacctgaattggtgtttctggcttcgttgatctgtaataggaacgcacagggttcctggagctgcccccttagttttcgaagt

upper sequence: GLYMA03G06440.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S282_25V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacagtactcacagttgttgatgatattatttgtcatttttatttgtaattttcgtttgaactcattttgcctggctgtgtag-------------
||  | || |||||||| || ||||||||||||||||| || || || ||||||||||||||||| ||||| ||||| ||  ||||  |  | |      || ||     | ||||| |     |  ||   || |   | |  | |  || |   ||||   ||              
GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGGATGCTTGACAAGCTGGGTGGCGCCTTCgtgagtaccattttgaactgaattcatacctatgtttgtgagcggaaggtg-gcttgtatctagtgcactgttagataggcttcttaaatgaaacttttgc

upper sequence: GLYMA03G06440.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S461_1V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacagtactcacagttgttgatgatattatttgtcatttttatttgtaattttcgtttgaact-cattttgcctggctgtgtag------------
||  | || |||||||| ||  |||||||||||||||| || || || ||||||||||||||| | ||||| ||||| ||  || |    | |     |    |      | |   || |  || |||  |||  |  | |      |||| ||   |  ||  | |            
GCTCGTGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTTGACAAGTTGGGTGGTGCCTTCgtgagttcctagcccttgacttcccacctatctctgcatcctcattttttaaaatccttttataggtggcattctgtg-gaatgaatcgcccacctacctt

upper sequence: GLYMA03G06440.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S38_194V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgt----acagt-actcacagttgttgatgatattatttgtcatttttat-ttgtaattttcgtt-tgaactcatttt-gcctggctgtgtag----
||  | || |||||||| || |||||||||||||||||||| | ||| ||||||||||||||| | ||||| ||||| ||| ||    ||  | ||  |   | | ||||| || || |  |  | |  |  | || | ||  ||| ||     |||||  || |  |          
GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCTCCCAGACATTGGATGCTTGACAAGTTGGGTGGTGCCTTCgtaagttctcacgttgacctaatttcgctgatgctagtactatttgtgtcgacgtcgtgagttaggttgtggttatatttttacccgaattctcttcgac

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|151396175|gb|EV266052.1|EV266052
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|192300483|gb|FG987910.1|FG987910
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|7284412|gb|AW597004.1|AW597004
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|9203665|gb|BE329889.1|BE329889
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|298196174|gb|HO044565.1|HO044565
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|9986822|gb|BE660930.1|BE660930
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|298190510|gb|HO032631.1|HO032631
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGTCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|13789053|gb|BG651644.1|BG651644
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|298186402|gb|HO037035.1|HO037035
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
EST: gi|17401982|gb|BM178764.1|BM178764
EST:     GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTT                         GCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG
genomic: GGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacag ... ggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAGAGGGTTGAAGAAACACTTGAAGAGGCTCAATGCTCCAAAACACTGGATGCTTGACAAGCTTGGTGGGGCCTTTgtatgtacagtactcacagttgttgatgatattatttgtcatttttatttgtaattttcgtttgaactcattttgcctggctgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG