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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttagagcttccagattttatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC

Basic information

species Glycine max
transcript GLYMA04G07570.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G07570.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttaga-gcttccagattttatctgct--tccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC
                                                                                                                                     | | ||||||| | ||    |   | ||| ||| ||    | |   ||||     |||| | || |||||||||| | ||||| ||||| ||||| || || || ||||| ||||| ||||| ||||||||||  || |||||||||||||| || || || ||  | 
-----------------------------------------------------------------------------------------------------------------------------------gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT

upper sequence: GLYMA04G07570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttagagcttccagattttatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC
                                                                                                  |||  |  ||   ||| ||   ||| | ||   ||| |       |  || |  |||||  |   ||  |  || || | || |  ||| |   |   ||||||||| ||||||||||||| |||||||| || || || || ||||||||||| |||||| ||||||| || |||||| ||||||| ||||| || || 
-----------------------------------------------------------------------------------------------gtgatattcttttagatatacag--caattagactcaaacat-----cagactgc--attttccaagactgacccatatt-tttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT

upper sequence: GLYMA04G07570.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 3
gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttagagcttccagattttatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC
                                                                                                         ||||||||     ||||  || | || | |     | |    ||      || |       |   |  |  |||  || | ||| ||   |||||||||| |||| |||||||| |||||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||||||
-------------------------------------------------------------------------------------------------------gtattgtttagt---acca--tttatcacattttgtcatttccattactcccttctgtgagaactcaacctattct--ttgcatttcctcatcagGTTATGTATAGTCTTTCTTACCTTTAGCTGTATCGGATATGCCATGCCGTTCATTCTATGTGCTACAATCTGCTGCTGCCTCCCTTGTATAATTTCCATC

upper sequence: GLYMA04G07570.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S74_109V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttagagcttccagattttatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC
             | || |     |   ||  ||   |||    ||  ||  |     |      |        |||| |    ||  |   |  |   ||   || |   |    |      |  ||  | |||  |||                 | ||||  |   || |     |            |||||||||||||  | ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || || || |||||||||||| |||| || |||||| |  | 
-------------gtaggtg----acgcagtgtggtgttgtgggaaggttggttggttgtggcggtggcctgtgaattgtggtgtgg-gtcggagatggtagtgaagt---tgcaaaggttgtggggagaagaatggacag----------------taagagggttgtgagtggggtt------------ttggcagGTTATGCATCGTGTTGCTTACGTTCAGCTGCATCGGATATGCGATGCCTTTTATTCTTTGCGCCACTATTTGCTGCTGCTTGCCGTGCATAATTGCACTG

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|208115710|gb|GD908589.1|GD908589
EST:     TGGATTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAG                         GTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
genomic: TGGATTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAGgtatagcctc ... tgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
EST: gi|207701551|gb|GD682880.1|GD682880
EST:     TGGATTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAG                         GTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
genomic: TGGATTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAGgtatagcctc ... tgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
EST: gi|192303661|gb|FG995983.1|FG995983
EST:     TGGATTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAG                         GTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
genomic: TGGATTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAGgtatagcctc ... tgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
EST: gi|192311756|gb|FK003589.1|FK003589
EST:     TTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAG                         GTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
genomic: TTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAGgtatagcctc ... tgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
EST: gi|192311755|gb|FK003588.1|FK003588
EST:     TTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAG                         GTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT
genomic: TTTTTGGAGGACATTCATCTGCTGATCAAGCACCTAACTTATACAGgtatagcctc ... tgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttctgattttttagagcttccagattttatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC
    ttctgat  putative branch site (score: 3)
                            ttttatctgcttcctt  putative PPT
       tgatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttagagcttccagattttatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC