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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccctctcctctttttttttcttccttttttttctctttatcaaatcttataattgttactatagtctaatctctggttttctatagtttacaa...

Basic information

species Glycine max
transcript GLYMA13G10640.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G10640.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G42050.1 (Arabidopsis thaliana), 5'ss of exon 1
CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccctctcctctttttttttcttccttttttttctctttatcaaatcttataattgttactatagtctaatctctggttttctatagtttacaa
|| ||| ||||  || |||| |  || ||||||||||| || ||||||||||| ||||||||||||||||||| |||||||||| || | ||||| || |||||    |  | | ||||| || ||  |  ||   ||  |  || |    | | ||  ||||    || |   | | | | |                 
CCTCCAGCAGAAGCTTTGCCAAGAAACGAAACCATTGGTGGTTACATCTTTGTCTGCAACAACGATACCATGGAAGAGAATCTCAAACGCCAGCTTTTCGgtattcatcaccacatctttcttcttactgtttcgattgtttcttcttggttttgat--ttgtggggatggaa-attgtttag-----------------

upper sequence: GLYMA13G10640.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 5'ss of exon 1
CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccctctcctctttttttttcttccttttttttctctttatcaaatcttataattgttactatagtctaatctctggttttctatagtttacaa-----
|||||||| |||||||| || |  ||||| ||| |||| || ||||||||||| |||||||||||||| |||  |||||||||| | |||||||||||||||| | ||||     ||| | ||| |||   | | ||| |  ||| |||       |  |||    |  | ||| || |||| ||| |  | ||    |      
CCACCATCGGAGTCTCTCCCCAGAAATGAGACCGTTGGTGGATACATCTTTGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagcccccg----tctctgtttctctgattctatttaccatttttcagtgtccttctttggggtttgattctgat-tctgttttgcgttggtgggtatctctc

upper sequence: GLYMA13G10640.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccctctcctctttttttttcttccttttttttctctttatcaaatcttataattgttactatagtctaatctctggttttctatagtttacaa
||||| || |||   || ||   |||||||||  |||| ||||| ||||||||||||||||| |||||||||  |||| | ||| |  | ||||||||||||| |||| ||||| |  ||| | |   |   ||  |  || |   | ||| ||| |  || || || | |     | || |                  
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttg--cgctttcag------------------

upper sequence: GLYMA13G10640.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ18285 (Selaginella moellendorffii), 5'ss of exon 1
CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccctctcctctttttttttcttccttttttttctctttatcaaatcttataattgttactatagtctaatctctggttttctatagtttacaa
||||| || |||   || ||   |||||||||  |||| ||||| ||||||||||||||||| |||||||||  |||| | ||| |  | ||||||||||||| |||| ||||| | |||||| |   |   ||  |  || |   | ||| ||| |  || ||  | |  |    | || |                  
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttttttttctgtctttcttcgtagctatgactgaaagcttgtt-ttttttttcttttgcgctttcag------------------

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|254331893|gb|GR846203.1|GR846203
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|151402959|gb|EV272772.1|EV272772
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|11273755|gb|BF324150.1|BF324150
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|58024390|gb|CX711131.1|CX711131
EST:     AACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: AACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|5057954|gb|AI736430.1|AI736430
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|151395760|gb|EV265637.1|EV265637
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|4396241|gb|AI495238.1|AI495238
EST:     AAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: AAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|15000771|gb|BI321585.1|BI321585
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|14990506|gb|BI316179.1|BI316179
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|11274747|gb|BF325082.1|BF325082
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|21600694|gb|BQ611025.1|BQ611025
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|12774159|gb|BG239086.1|BG239086
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAAATAACTCCAGGGTTG
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAA-TAACTCCAGGGTTG
EST: gi|4313652|gb|AI460771.1|AI460771
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|254331894|gb|GR846204.1|GR846204
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|11413917|gb|BF425928.1|BF425928
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|10843221|gb|BF066529.1|BF066529
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|4301736|gb|AI443233.1|AI443233
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|58017712|gb|CX704454.1|CX704454
EST:     AACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: AACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
EST: gi|58018450|gb|CX705192.1|CX705192
EST:     TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTG                         GTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC
genomic: TGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccc ... tgctctgcagGTCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccctctcctctttttttttcttccttttttttctctttatcaaatcttataattgttactatagtctaatctctggttttctatagtttacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctcc