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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGCTAGGGAGTAAGAGATGGATTTGGACCAGTGGATCTCCAAGGTGAAGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgcatatgcatattttctccttttccttttagggtttcagttactgcccgcgcttcccttttctcttctctaagtccgtcaaatgttcaaacg...

Basic information

species Glycine max
transcript GLYMA0048S00290.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 1
-GCAAGCTAGGGAGTAAGAGATGGATTTGGACCAGTGGATCTCCAAGGTGAAGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgcatatgcatattttctccttttccttttagggtttcagttactgcccgcgcttcccttttctcttctctaagtccgtcaaatgttcaaacg------
  |  || ||    |    |||||||||||| | ||||||||| ||||||||||| |||||||||||   |||  | ||||| ||    || |||||||| ||    || | |   |       | || | |||    |  | ||| |||| |        | || |   |  | ||||  |  || |    |      ||      
CCCCCGCGAGCCCCTCCC-GATGGATTTGGATCTGTGGATCTCTAAGGTGAAGGAGGGCCAGCACCTCGCCGAGCACGAGCTCCAGTCCCTCTGCGAATACgtgagctttcctcccc-----cccgccctgtcccccgattggttcggttattagggtttttgccatgccccgtgctctc-gcgcggcggcggcggcggcggcgcgc

upper sequence: GLYMA0048S00290.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G055905_T02 (Zea mays), 5'ss of exon 1
-----------------------------GCAAGCTAGGGAGTAAGAGATGGATTTGGACCAGTGGATCTCCAAGGTGAAGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgcatatgcatattttctcctttt-ccttttagggtttcagttactgcccgcgcttcccttttctcttctctaagtccgtcaaatgttcaaacg
                             |   ||    |     |  |||||| |||| | ||||||||||||||| ||||| |||||||||||   |||  | ||||||||    || |||||||| ||   |    |       | | |||| ||   ||  |||||||||  |||||  |    |||  ||    |                              
GCCCCTCCGCCTCAAATCCCACGCGCCCGGTTGGCCGCCGCCCCCGCCATGGATGTGGATCTGTGGATCTCCAAGGTCAAGGAGGGCCAGCACCTCGCCGagcacgagcttcagtcgctctgcgaatacgtgagtccctaccctttgactctctcgttccgccccttagggtttttgttacctcgt-tgctctccagggcg-----------------------------

upper sequence: GLYMA0048S00290.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G055905_T05 (Zea mays), 5'ss of exon 1
GCAAGCTAGGGAGTAAGAGATGGATTTGGACCAGTGGATCTCCAAGGTGAAGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgcatatgcatattttctcctttt-ccttttagggtttcagttactgc-ccgcgcttcccttttctcttctctaagtccgtcaaatgttcaaacg
|   ||    |     |  |||||| |||| | ||||||||||||||| ||||| |||||||||||   |||  | ||||||||    || |||||||| ||   |    |       | | |||| ||   ||  |||||||||  |||||  |   || || |                ||  |      ||  |     
GTTGGCCGCCGCCCCCGCCATGGATGTGGATCTGTGGATCTCCAAGGTCAAGGAGGGCCAGCACCTCGCCGAGCACGAGCTTCAGTCGCTCTGCGAATACgtgagtccctaccctttgactctctcgttccgccccttagggtttttgttacctcgttgctctccagggcggcggcacacgagcacacagcttgcgcggc--

upper sequence: GLYMA0048S00290.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 1
GCAAGCTAGGGAGTAAGAGATGGATTTGGACCAGTGGATCTCCAAGGTGAAGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgcatatgcatattttctccttttccttttagggtttcagttactgcccgcgcttcccttttctcttctctaagtccgtcaaatgttcaaacg--
   |  ||| |||  ||  ||||||||||| || ||||| |||||||| || ||||| ||||| ||   |||||| |||||||| ||||| |||||||| |||    | | | | | | || |      ||  |||      ||     | |   |    |   || |||||| ||    ||  |     | || | |    
TATATATAGAGAGAGAGTTATGGATTTGGATCAATGGATTTCCAAGGTTAAAGATGGTCAGCATCTCTCCGAAGACGAGCTTCAGCTTCTCTGCGAATACgtacgccttcttcttcttcttcttcttacttgatttcttctcttggtcgattaagcttcttgtgctcttctctgctt--ggtttgatctgtatttatatacc

upper sequence: GLYMA0048S00290.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 1
GCAAGCTAGGGAGTAAGAGATGGATTTGGACCAGTGGATCTCCAAGGTGAAGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgcatatgcatattttctccttttccttttagggtttcagttactgcccgcgcttcccttttctcttctctaagtccgtcaaatgttcaaacg---
    | |  |  ||  |  ||||||||||| |||||||| |||||||| || || |||||||| || || ||||| ||||| || ||||| |||||||| |||  ||| | || |  | | ||||  || |  |||      | |    | | |||     |   |||| | || | ||| |  || |  | ||     |   
-AGGGTTTTGTTGTTGGGAATGGATTTGGATCAGTGGATTTCCAAGGTCAAAGAAGGCCAGCATCTCCTGGAAGACGAGCTCCAGCTTCTCTGCGAATACgtacgttttc-taggtttttgttctttttcttgtttgcttcctccgaaaattacccaaatcttgatttttt-ttttataattatgt-atttatttctctggtt

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|193398959|gb|FK363859.1|FK363859
EST:     CTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: CTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|209728247|gb|BW651682.1|BW651682
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|298172509|gb|HO019549.1|HO019549
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|151410851|gb|EV280666.1|EV280666
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|213603385|gb|DB966616.1|DB966616
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|192323250|gb|FK018961.1|FK018961
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|298178347|gb|HO024082.1|HO024082
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGGGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|207708160|gb|GD692012.1|GD692012
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|192296025|gb|FG989419.1|FG989419
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|298187406|gb|HO034555.1|HO034555
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|209707319|gb|BW670611.1|BW670611
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|208275394|gb|GE079386.1|GE079386
EST:     CTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: CTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|298190555|gb|HO032676.1|HO032676
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|298188878|gb|HO035571.1|HO035571
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAG                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCG
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
EST: gi|308098123|gb|HO761294.1|HO761294
EST:     AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATAT                         GTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA
genomic: AGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgc ... aacatttcagGTTAAAGAGATCCTTATTGAGGAGTCAAATGTGCAGCCTGTCAACAGTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGCTAGGGAGTAAGAGATGGATTTGGACCAGTGGATCTCCAAGGTGAAGGATGGCCAGCACCTTCTCGAAGAGGAGCTTCAACTTCTTTGCGAATATgtatttttgcatatgcatattttctccttttccttttagggtttcagttactgcccgcgcttcccttttctcttctctaagtccgtcaaatgttcaaacg

- - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccgcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccttttc