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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGAACATTATCGAGGACCGAAGCTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctccttctttctctgtttgtattaatgagctactgatatcttaataattttgaaatcggatgttgtggtaatatatagtaaagttacttttgaattccttgatccttagttagtctgttttgttattcaggtgttgattgcatcaggatgttatgactaatgtattctatcattcag

Basic information

species Glycine max
transcript GLYMA20G37170.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37170.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G04870.2 (Arabidopsis thaliana), 5'ss of exon 3
ACCAGAACATTATCGAGGACCGAAGCTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctccttctttctctgtttgtattaatgagctactgatatcttaataattttgaaatcggatgttgtggtaatatatagtaaagttacttttgaattccttgatccttagttagtctgttttgttattcaggtgttgattgcatcaggatgttatgactaatgtattctatcattcag
 || | ||  ||    ||||| ||||||||||| || ||||| ||||||||||||||||||||||| ||||| || || ||  ||||||| || |||||||| |     | ||||    |  |||| |  ||     | |  |   |  |||  | || ||||     | ||| |  | |  ||                                                                                                   
GCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGTAGAGCTTCTGGATCAGGGTCACGAGgtgtttactcctcttctgttagttgtttatatatttgatt--tggttacatacatgtgtaatca----tcgtgattgt-ttcag---------------------------------------------------------------------------------------------------

upper sequence: GLYMA20G37170.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 5'ss of exon 2
ACCAGAACATTATCGAGGACCGAAGCTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctccttctttctctgtttgtattaatgagctactgatatcttaataattttgaaatcggatgttgtggtaatatatagtaaagttacttttgaattccttgatccttagttagtctgttttgttattcaggtgttgattgcatcaggatgttatgact-----aatgtattctatcattcag
||| ||||| ||| | ||||| ||||| || ||||| || ||||||||||| |||||||||||||||||||||||||| || ||||||||||| |||||||||| | |  |   |     | |    |  |||      ||  || |     | ||| |||    |  |        | |  ||  |||||  |||  || |       |||| | |  | |   || |   |  | || |  || ||||||||    ||   |     ||||  ||   |  |||||
ACCTGAACACTATAGGGGACCAAAGCTCAAGGTGGCTATCATTGGAGCTGGGCTTGCAGGCATGTCAACTGCAGTGGAGCTTTTGGATCAAGGCCACGAGgtttggattatatatgtaaagatatgttggatgtatctttggcatttatcatactttcaaacaaaacatgaattagtttttcagctaagtttgtttcaaaatggaattcccttggatgattttaattttggctttgctgatt-ttccatcaggagaaaattggtttataaatggtttggtttgttcag

upper sequence: GLYMA20G37170.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S211_145V6.1 (Physcomitrella patens), 5'ss of exon 2
ACCAGAACATTATCGAGGACCGAAGCTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctccttctttctctgtttgtattaatgagctactgatatcttaata-attttgaaatcggatgt-tgtggtaatatatagtaaagttacttttgaattccttgatccttagttagtctgttttgttatt-caggtgttgattgcatcaggatgttatgactaatgtattctatcattcag
||| |||   ||   |||||| ||||| |||||||| || ||||| ||||| || || |||||||| ||||| ||||| ||  | || ||||||||||||||   ||| ||| |       || | |||| ||  ||     | || ||||   |||  | ||| |  || ||||||         | ||||| ||   ||  |  |||||   |||   | |||  |  | |     |||| |||| |      |                              
ACCCGAAACCTACAAAGGACCCAAGCTCAAAGTGGCCATCATTGGCGCTGGTCTCGCTGGCATGTCCACTGCCGTGGAGCTTCTCGAGCAAGGACACGAGgt---gctgctt-tggacggattcgcattactgt-ctgggattttcctaatgtgtttcaatatcagcggtctgtggtc--------tgaagttgctgccgaggta-ttgatttgtag---gcctgggtgttgaccatgggtgatgatggtgcacag------------------------------

upper sequence: GLYMA20G37170.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S149_171V6.1 (Physcomitrella patens), 5'ss of exon 2
ACCAGAACATTATCGAGGACCGAAGCTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctccttctttctctgtttgtattaatgagctactgat-atcttaataattttgaaatcggatgttgtggtaatatatagtaaagttacttttgaattccttgatccttagttagtctgttttgttattcaggtgttgattgcatcaggatgttatgactaatgtattctatcattcag
 || ||    ||   ||| ||||||||||| || || || ||||| ||||| ||||| |||||||| || |||||||| || ||||| ||||| ||||||||   | | || |   ||||| | | |||  | |  | | | |  | || |  |||    | ||   || | |   |||||  |      || | ||  ||||   |||      ||| |    ||||  |    ||   ||||  |||  |  ||  | |   |  ||||             
GCCCGAGGCGTACAAAGGTCCGAAGCTGAAGGTTGCGATCATTGGCGCTGGGCTTGCTGGCATGTCTACGGCAGTGGAGCTTTTGGAGCAAGGCCACGAGgt---gattctccc--ctctggtggcattc-tcaattgcagtttgtgtttaggattccttactctcttggtttttcaatatcaaaggtcattgcattgaaattg--tgaaagaaggtttgatgtttttcgtgccaagaatttga--gcactaatataatgt---ttgtgtag------------

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|209716760|gb|BW682242.1|BW682242
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
EST: gi|209724167|gb|BW659701.1|BW659701
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
EST: gi|20497971|gb|BQ272901.1|BQ272901
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTC
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTC
EST: gi|151412615|gb|EV282427.1|EV282427
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
EST: gi|213611643|gb|DB969031.1|DB969031
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
EST: gi|213605385|gb|DB964580.1|DB964580
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
EST: gi|209703397|gb|BW676224.1|BW676224
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
EST: gi|209697794|gb|BW663938.1|BW663938
EST:     GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTAT
genomic: GACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTAT
EST: gi|193421144|gb|FK389135.1|FK389135
EST:     CATGTCAACTTGTCAGTGGAACTCTTGGATCAAGGACACGAG                         GTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT
genomic: CATGTCAAC-TG-CAGTGGAACTCTTGGATCAAGGACACGAGgtttagctcc ... tatcattcagGTGGATATATATGAGTCAAGGCCTTTTATTGGTGGCAAAGTTGGTTCTTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGAACATTATCGAGGACCGAAGCTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGTGGAACTCTTGGATCAAGGACACGAGgtttagctccttctttctctgtttgtattaatgagctactgatatcttaataattttgaaatcggatgttgtggtaatatatagtaaagttacttttgaattccttgatccttagttagtctgttttgttattcaggtgttgattgcatcaggatgttatgactaatgtattctatcattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA