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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtcttccaaactttacctgctgacacattgttcaatcaaaacatttactgactaccctcactttgatattttag

Basic information

species Glycine max
transcript GLYMA10G29250.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 8
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtcttccaaactt----tacctgctgacacattgttcaatcaaaacatttact--gactaccctcactttgatattttag---------------------
||| || ||||||||||||||  ||||||| |||||||||||||| || || ||||||||||| || |||  |||||||||||||||| ||||  | || ||  |||   | |  ||| |    |  ||  | |   | |||| | |||   ||||| ||      | || ||  |  ||  ||||                      
TGCTGACATTCTTGATCCTGCTTTGATGCGATCTGGTCGTTTGGACCGAAAGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtt---tccagaacctgtgatgtctaatcagctaatgtttattcatc-catttgcttttgtaatccacaagtc-atgctttaactaatatgtggttctctgtag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 8
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgt-----cttccaaactttacc-tgctgacacattgt--tcaatcaaaacatttact----gactaccctcactttgatattttag-------
||| ||||||||||||||||| |||||| | ||||||||| |||| || || |||||||| || || |||   || |||||||||||| |||| || ||||| | |||      |  | ||| | |    | ||  | || | |   |   |  |  |||| ||     |||      |  ||      | ||       
TGCTGATATTCTTGATCCTGCTCTGATGAGATCTGGTCGTCTGGACCGGAAGATTGAGTTCCCTCATCCATCAGAGGAAGCAAGAGCTAGAATCCTGCAGgtattttgctcgggccactaaaatatgttgtactagctcagtatggcctcccccagtatttgctccaaaactgttgatatcttcccccctaaggtctagt

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 7
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgtt---gtcttccaaactttacctgctgacac--attgttcaatcaaaacattta-ctgactaccctcactttgatattttag---------------
||| || || ||||| ||||| |||||||| ||||| || ||||| || || |||||||| || ||||||   ||||||||||||||| ||||  | || ||  ||           |  ||  |  ||||||      |   |   |     || |   |    || |   |||    | || |                 
TGCTGACATCCTTGACCCTGCTCTGATGCGATCTGGACGGTTGGACCGAAAGATTGAGTTCCCTCACCCATCCGAAGAAGCAAGAGCTAGAATCTTGCAAgtcggtctcaacaacttatgctcaaattgctgaagtttgtcagtggctttcctcagtaggccatttatcacaactaacgtgttctgtattggtcctctgtag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtcttccaaactttacctgctgacacattgttcaatcaaaacatttactgactaccctcactttgatattttag---------------------------------------------------------------------------------------------------
||| ||||| || ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| | ||||||||| ||||   | ||  ||||||||   | || |  |     |   | ||      ||  |  ||    |  |    | |   |    | |       || |                                                                                                    
TGCTGATATACTAGATCCTGCCCTTATGCGTTCTGGTCGTTTGGATCGTAAAATCGAGTTTCCGCACCCCACTGAAGAAGCTAGAGGCAGGATCTTACAGgttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtcttccaaactttacctgctgacacattgtt-caatcaaaacatttac------tgactaccctcactttgatattttag
|||||||||||| || || || || |||||||||||||| || ||  | || |||||||| ||||||||||  |||||||| |||||  ||||  | |||||||||  ||| |||   || |     |||| | | ||   ||  ||||   |  |        |||| ||  |||     | |  ||
TGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAGCGAGAGCAAGAATCTTGCAGgtttgtc-tctcccatttttcaaaca-tgacccttggtgataagtaaaaggctctcataacacaactaacccaactgaatgaatccag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 8
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtcttccaaactttacctgctga------cacattgttcaatc-----aaaacatttactgactaccctcactttgatattttag
 || |||||||| || ||||| || ||||| |||||||| |||||||||||||||||||||||||| || | |||||||||||||||||||||  | ||||| |||  ||    ||  ||| | |   ||      ||||||| ||| ||     | | |  ||| ||||| |  |||| |||   || |||
AGCTGATATTCTGGACCCTGCACTTATGCGATCTGGTCGATTGGATCGTAAAATTGAGTTTCCACATCCCACTGAAGAAGCAAGAGCTCGAATCTTGCAGgtatgtcttcaatgaatattttcttctagatcattacacattgatcactctttgcagagctcttattgact-ctttcacattgtatttgtag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgt-----------tgtcttccaaacttta---cctgc-tgacacattgttc--aatcaaaacatttactgactaccctcactttgatattttag--------------------------------------------------------------------------------
 ||||||||| | || |||||  ||||||||||||| ||||||||| | || ||||||||||| || ||||  || || ||| ||||||| ||| | |||||| |             |  |   | |||||      ||| | |  |  |   |  || | || ||| |  | ||  |  |   |||  | ||| |                                                                                 
AGCAGATATTTTGGACCCTGCTTTGATGCGTTCTGGACGTTTGGATAGGAAGATTGAGTTTCCTCATCCAACGGAGGAGGCACGAGCTCGTATTTTGCAGgttcggataaacaatagcgcttggtagactttgaagtttgcataatcctgtacccctaacctaaccatgttttcac--ctattgttttactgtttgatccttctataattataccacctatacagatttttatgagcaggatatcttatcaatcactgtaatgaactttcacctccag

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|23732877|gb|BU764614.1|BU764614
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|4397504|gb|AI496501.1|AI496501
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|6847857|gb|AW350147.1|AW350147
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|58017156|gb|CX703898.1|CX703898
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTTTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|254342561|gb|GR858723.1|GR858723
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|6482334|gb|AW201601.1|AW201601
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|7232532|gb|AW567887.1|AW567887
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAA
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAA
EST: gi|4307528|gb|AI444060.1|AI444060
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|9901285|gb|BE610253.1|BE610253
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATGCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
EST: gi|298195294|gb|HO043822.1|HO043822
EST:     AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAG                         ATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT
genomic: AAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtc ... gatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAGCAAGAGCTCGAATTCTACAGgtttgttgtcttccaaactttacctgctgacacattgttcaatcaaaacatttactgactaccctcactttgatattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT