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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacatacatgaatgatgatgcatgccctttctagttcaagattattaggataggataattgcatgaaattacgactttgccctcaagttgaagct...

Basic information

species Glycine max
transcript GLYMA04G42800.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 5'ss of exon 1
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacatacatgaatgatgatgcatgccctttctagttcaagattattaggataggataattgcatgaaattacgactttgccc-tcaagttgaagct-
||| || || || || || || ||||||| ||| ||||||||||||||||| || |||||||| || || |||||||  ||||| ||||||| |||  ||||||||| ||||   | | || |   |   |   | |  |   |  | || |   |   ||  |   | ||| |     ||  |    ||||||| |  |  
CGCCGGCAAGGCGCCCAAGGGCGACAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCCGCAAGAAGAACACCCTCCGGgtacatatatacgccattaattaattacctcgaatttgctcttaattcatcaaattcaaat--tcagacgaattctactctcagttaatcaagtttagacaa

upper sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 5'ss of exon 2
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacatacatgaatgatgatgcatgccct---ttctagttcaagattattaggatag-gataattgcatgaaattacgactttgccctcaagttgaagct
||| || || || || || || || |||| ||| ||||||||||||||||| || |||||||| || || |||||||  ||||| ||||||||||| ||||||   | | ||   |   | ||| |   | ||   |||      ||   | |    || | ||| ||||  | |  |    || |     |       |    
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCCGCAAGAAGAACAGCCTCAGGgtaagcaaaaaccacacccaagattccatcactaaattcattactaaatctgtgttcatcgtgattattgattaatttagtcacctaattattcgcccaa----

upper sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 5'ss of exon 2
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacata----catgaatgatgatgcatgccctttctagtt-caagattattaggataggataattgcatgaaattacgactttgccctcaa-gttgaagct----------------
                      | ||||| ||| ||||||||||||||||| || |||||||| || || |||||||  |||     | |    ||    || |   || |    | | |  | |  |   | |   || || || |    || |    ||   || ||  | ||   | |    |||  |||||     |||  |                
---------------------CGTCAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGC-CGCCGCCCGCAAGCTCTCCAAGTCCTCCCACAACGCCCTCAGGgttagtatttacttcttttaattacttacttctcctaatctaatcatctcttgctttcaatcatttctcctcaccaacgaatttacccccattttatttt

upper sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G014653_T02 (Zea mays), 5'ss of exon 1
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacataca-tgaatgatgatgcatgccctttctagt-tcaagattattaggat---aggataattgcatgaaattacgactttgccctcaagttgaagct
||| || || || || || || || |||| ||| ||||||||||||||||| || |||||||| || || ||||| |  ||||| ||||||||||| ||||||   |||  |  |         | | | |      | |  ||   |   |    ||   |  | ||   | ||    ||     | ||  ||    ||     
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCGGCGCGCAAGAAGAACAGCCTCAGGgtaagaacaagcgctccgccgccgtccgtccgtccgttggcgtcgtcaccgtccaaatcaaacaaaaagaacttggcgataatgtgtcgctttcgtaatg-----

upper sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAA---CAGCCTAAGGgtacatacatacatgaatgatgatgcatgccctttctagttcaagattattaggataggataattgcatgaa-attacgactttgccctcaagttgaagct
    || |||||||| || || || || | ||||||||||||||||||||| ||||||||||| || || || ||||||||||| |||||    || || ||||||   |   | ||   ||||    |||     ||  | |      ||  |      ||  ||||| || ||   |     |||   | ||          
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGgtatggaatcagatc--tgatt-cacatctttgtttcaatctcttgtt-ctgtttctggtaaattgaatcaacggtgttgatttttgcccag---------

upper sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ20531 (Selaginella moellendorffii), 5'ss of exon 1
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGAT-GTAG-ATCGCTCCGTTCGCAAAAAGAACAGCC-----TAAGGgtacat-acatacatgaatgatgatgcatgccctt-tctagttcaagattattaggataggataattgca-tgaaatta-cgactttgccctcaagttgaagct----------
                        |||||  |||||||||||||||||||| || ||||||||| | ||   |    |   ||||   |   | |||      |||     ||  |  |    ||  |  ||    | | |   ||   ||| |  |  |    |    |  |||   ||||||   ||| ||     | || ||   | |          
---------------------ATCCAAGACGAATTGGATCATGCACGAGTACCGCCTCGCCGATAGCAGCGCCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGGgtaagaagaatctccgtcatcgcctcagtcatggcttctttcttgcattctttgtggtgaaatcctcgatttcctggtgaaattcgcgtttcttgcttga

upper sequence: GLYMA04G42800.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ28600 (Selaginella moellendorffii), 5'ss of exon 1
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGAT-GTAG-ATCGCTCCGTTCGCAAAAAGAACAGCC-----TAAGGgtacat-acatacatgaatgatgatgcatgccctt-tctagttcaagattattaggataggataattgca-tgaaatta-cgactttgccctcaagttgaagct----------
                        |||||  |||||||||||||||||||| || ||||||||| | ||   |    |   ||||   |   | |||      |||     ||  |  |    ||  |  ||    ||| |   || | ||| |  |  |    |    |  |||   ||||||   ||| ||     | || ||   | |          
---------------------ATCCAAGACGAATTGGATCATGCACGAGTACCGCCTCGCCGATAGCAGCGCCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGGgtaagaagaatctccgccatcgcctcggtcatggcttctttcttgcattctttgtggtgaaatcctcgatttcctggtgaaattcgcgtttcttgcttga

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|17401487|gb|BM178269.1|BM178269
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACA-CAAGAAGGGCA
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCA
EST: gi|254345506|gb|GR851668.1|GR851668
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|19453464|gb|BM954874.1|BM954874
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAAGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|15812832|gb|BI785107.1|BI785107
EST:     TCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAAGG                         T-AGATGATTGGGTGCTTTGGCGTATT
genomic: TCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAA-GGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATT
EST: gi|209708546|gb|BW668157.1|BW668157
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGC
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGC
EST: gi|254314898|gb|GR829891.1|GR829891
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|20811624|gb|BQ296102.1|BQ296102
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|16105655|gb|BI893395.1|BI893395
EST:     ATCGTCTCGCCGATGTAGATC-CTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCTGTATTTACAACAAGAAGGGCACGATCGA
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCC-GTATTTACAACAAGAAGGGCACGATCGA
EST: gi|19453545|gb|BM954955.1|BM954955
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|20811728|gb|BQ296206.1|BQ296206
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|298181418|gb|HO022857.1|HO022857
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCG
EST: gi|19270236|gb|BM886492.1|BM886492
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|298179565|gb|HO028036.1|HO028036
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCG
EST: gi|298184586|gb|HO029799.1|HO029799
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTT
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTT
EST: gi|254319224|gb|GR830572.1|GR830572
EST:     ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGG                         TTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacat ... gattatgcagTTAGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAGGGAAAGCTCCGAAAGGGGACAAGAGCAATTGGATCATGCACGAGTATCGTCTCGCCGATGTAGATCGCTCCGTTCGCAAAAAGAACAGCCTAAGGgtacatacatacatgaatgatgatgcatgccctttctagttcaagattattaggataggataattgcatgaaattacgactttgccctcaagttgaagct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctcaa