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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtctttaattcttgttatctatatgttttttctgattgacattatataagtatgcttcagagaattttgctttctttgggtaaagcataatagttt...

Basic information

species Glycine max
transcript GLYMA10G29250.1
intron # 7
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 7
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 7
TGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtctttaatt-----cttgttatctat-atgttttt-----tctgattgacattatataagtatgc---ttcagagaat-----tttgctttctttgggtaaagcataatagttt----------------------------------------------------------------------------
|||||| ||||| || ||||| || ||| | || ||||| |||||||| || ||||||||||| |||||||| |||||  |||| |||||  |  || ||       | | |||  ||| |   | ||     | ||  | |  || | |     |||   || |||   |      || | |   |||   |    || | || |                                                                             
TGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAGgtcagcattcaacctcaaacctattagttattacagtcttgatgctttgtctcaggttttgttcagttgcaggttgagaaggtataaagttacctctattgatcatgatatgagagatagatgaactgatattttttcccaatgtcttatttaatatctggtgtactaaacgtttgattgttgtgtggcttacag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 7
TGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtctttaattcttgttatcta-tatgttttttctgattgacattatataagtatgcttcagagaattttgctttctttgggtaaagcataatagttt
|||||| |||||||| || ||||| || || || ||||| || ||  | |||||||||||||| |||||||||||||| || || |||||||   | |  |     ||   || |  | |||||   |    |||| | |   |    | |  |  | ||   ||   |||| |   ||     | |  
TGAAGTGAGTGGAGATAGGGAGGTGCAGCGGACAATGTTGGAGTTATTGAATCAGCTTGATGGCTTTAGCAGTGATGATCGCATAAAGgttttattgttttctaaattcattactgcgcttttttccacct-cattttctggctcaagtccccatgaattcatttgtgttggattctgctatccactgc

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 7
TGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtctttaa---ttcttgttatctatatgttttttctgattgac-attatataagtatgcttcagagaattttgctttctttgggtaaagcataatagttt-
|||||||||||| ||  | || |||||  |||||||||| || |||||||||||| | || |||||||||||||| || || || |||||  |   | ||   || |||| || | ||  || | | |  || |   || |  || | ||   | |     | ||| |  ||    |     || || |  | 
TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtgaaggatttttgtcat-tctacattgtatgtagttaattgttttccaaatgtg---cgggtggctctgcatg-ttgatattgtatatgattgggta

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 7
TGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtctttaattcttgttatc-tatatgttttttctgattgacattatataagtatgcttcagagaat-tttgctttctttgggtaaagcataatagttt----------------------------------------------------------------------
|||||||||||||||  | || || ||  |||||||| | || |||||||||||||| ||||| || ||||||||||| || || || ||  | ||| || | |  ||||  | | |   || |     | |   | | | |  |||||  |     |  |||  |    |  || |||  | |     |                                                                      
TGAAGTAAGTGGAGATCGTGAAGTGCAGAGAACTATGCTGGAGTTGCTTAATCAGCTGGATGGATTCAGCAGTGATGAGCGCATTAAAgtgagccttgaaatatcattattatttctccattcttcacataatgatttctcaa-atgctctattatttgcttgtctataatcagtcaaggttgaagtcctagtcgtgggtgtagccgtgcgggctgaggaggaaattttaggaactaattcttgaatgtttcatgaacag

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:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|6847857|gb|AW350147.1|AW350147
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|58017156|gb|CX703898.1|CX703898
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|193451342|gb|FK420562.1|FK420562
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|254342561|gb|GR858723.1|GR858723
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGGGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|4290740|gb|AI437520.1|AI437520
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|6482334|gb|AW201601.1|AW201601
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|7232532|gb|AW567887.1|AW567887
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCCT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|4307528|gb|AI444060.1|AI444060
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|22525777|gb|BU084588.1|BU084588
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|9901285|gb|BE610253.1|BE610253
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
EST: gi|298195294|gb|HO043822.1|HO043822
EST:     TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG                         GTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT
genomic: TAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtcttt ... taaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtctttaattcttgttatctatatgttttttctgattgacattatataagtatgcttcagagaattttgctttctttgggtaaagcataatagttt

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