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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgattcataaacattttgtttccactgcagtgttgtcgaatctgtttcaatgaacaaccgatttcattttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT

Basic information

species Glycine max
transcript GLYMA02G32780.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G32780.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g41580.1 (Oryza sativa), 3'ss of exon 5
-------gtttgttgattcataaacattttgtttccactgcagt--gttgtcgaatctgtttcaatgaacaaccgatttcattttcttcctt-attttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT
        | |  |||||  |     |  | || | |  | | |   ||    ||      || || || ||  |   ||  ||  | |||| | ||  |||   ||| || || || |||||||||||||| ||||| ||| |||||||||| ||  |||| || |||||||| ||||| ||||| || ||||| | | |
tagatatatctactgattattcctattcctattcctatggtatttgattccataacgccggtctat-aataattgtcctctcttcttccctttacttgaagGGAGTGCACCACTTACTGCTGTTCAGTTGCTATGGGTGAACATGATTATGGATACGTTGGGAGCCTTGGCCTTAGCCACAGAACCACCAAATGACGAAAT

upper sequence: GLYMA02G32780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgttgattcataaacattttgtttccactgcagtgttgtcgaatctgtttcaatgaacaaccgatttcattttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT
||  |       | || || |      |||   |  | || | |  | || |  |||  |  | | ||||| |||  || |||  || ||||||||||||| ||||| ||||| ||  |||||||||||||| |||| |||||||| || ||||| |||||  | || || |||||||||||||| ||  |
gtacgacag--aaaaaccaatcaaacaccat--ctttcttctagcgtttggtcaaatatagtaaccatttcttttggtttctt--ttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT

upper sequence: GLYMA02G32780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G57330.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgttgattcataaacattttgtttccactgcagtg-ttgtcgaat--ctgtttcaatgaacaaccgatttcattttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT
||  ||  | ||| | ||||      |   |  || || || | ||||  | |||||| | |          | ||| | || |   |||||||||||||| || ||||| || || ||  |||||||||| ||| |||| |||||||| || ||||| |||||  | || || ||||||||||| || ||  |
gtaagtaaaatcaaacacatgcacaattttcaccaatgatttttgaataacagtttcagtaa----------tgattgttttgcaccttttcagGATCTGCGCCACTCACCGCAGTGCAACTGCTTTGGGTGAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCGACCGAACCTCCCAACGAAGGTTT

upper sequence: GLYMA02G32780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------gtttgttgattcataaacattttgtttccactg-cagtgttgtcgaatctgtttcaatgaacaaccgatttcattttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT
                                             || ||  | | |   |||  | |  | |    ||       | |   || |   |  || ||        || ||       |  |||||||||||| ||| | || ||||| |||||||||||||||||| |||||||||||||||| ||||| ||||| ||||| || |||||||| || |||| |||
gtgcgttggcccatggagctagtcttttcatttcatgtagtgctcttatttgtacttttgcataatatgccaatcaacaacagcagcaataatgataataataataatgataaggatctttgaaacaacattcagGATCTGCCCCCTTTACGGCTGTCCAGTTGCTTTGGGTCAACTTGATTATGGACACTCTCGGTGCATTGGCATTGGCGACAGAACCTCCAAACGATGCACT

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|208317976|gb|GE116701.1|GE116701
EST:     TTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGG
genomic: TTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193668302|gb|FK612638.1|FK612638
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|208322224|gb|GE122181.1|GE122181
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193591252|gb|FK546465.1|FK546465
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193602895|gb|FK555420.1|FK555420
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|151405499|gb|EV275313.1|EV275313
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|208283086|gb|GE077334.1|GE077334
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193363344|gb|FK326238.1|FK326238
EST:     TTGCTCTGATTA-TAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGG
genomic: TTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193452619|gb|FK417583.1|FK417583
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193521913|gb|FK480806.1|FK480806
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193658824|gb|FK607269.1|FK607269
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193641441|gb|FK589019.1|FK589019
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|254325639|gb|GR838520.1|GR838520
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|208151547|gb|GD946510.1|GD946510
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCA
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCA
EST: gi|208083780|gb|GD881728.1|GD881728
EST:     GTCAATATTGTTGCTCTGATTATTAACTTTGTTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: GTCAATATTGTTGCTCTGATTATTAACTTTGTTT-CTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|193571246|gb|FK532253.1|FK532253
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAAC
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAAC
EST: gi|208176837|gb|GD977686.1|GD977686
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|208174266|gb|GD971237.1|GD971237
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|208206601|gb|GE002462.1|GE002462
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG
EST: gi|5057752|gb|AI736228.1|AI736228
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTTACAGCTG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTG
EST: gi|14999736|gb|BI320550.1|BI320550
EST:     AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAG                         GATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGG
genomic: AGTCAATATTGTTGCTCTGATTATTAACTTTGTTTCTGCATGCATCACAGgtttgttgat ... ttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtcgaatctgtttcaatgaacaaccgatttcattttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT
                               tttcattttcttcctt  CT-rich tract
                              atttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgattcataaacattttgtttccactgcagtgttgtcgaatctgtttcaatgaacaaccgatttcattttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA