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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtattctgttttactaagaaatttttctgtatttatctgctcttcacctcactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG

Basic information

species Glycine max
transcript GLYMA05G26630.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G26630.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 3'ss of exon 8
gtctgtattctgttttactaagaaatttttctgtatttatctgctcttcacctcactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG
                        | | |  | |||   |    |||   ||  | |     | ||   | |     | ||     || |   |||| | ||  ||||||| |||||||| ||||||||||||||  ||||| | |||||||| || |||
----------------------gtactatcttttatcattggcttctattccagaattaatactttagataatttgcatttctaacacatctactttttcat--agGTTGGATATGTGACAACCATATGCTTTTCTGGCTTCTTGATCAGATGCGTAATG

upper sequence: GLYMA05G26630.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G003076_T03 (Zea mays), 3'ss of exon 8
gtctgtattctgttttactaagaaatttttctgtatttatctgctcttcacct-cactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG
                    | |   |  | | | ||  |||| | ||       | | ||   |    | ||| |  | |   | |  |||       |||||||||||||||||||||||||||| || ||||| || ||| | ||||||||||| |||
------------------gtacactctggtttctgttggtctgatttttttaggtatttctgtacaaattatacactaattctgtat-tctgcataccataatgcagGTTGGCTATGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATG

upper sequence: GLYMA05G26630.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 9
gtctgtattctgttttactaagaaatttttctgtatttatctgctcttcacctcactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG
             |   ||  | | | |    || |  || |    ||      | | ||   |    | ||| |  | |   | | |   ||   |||| | |||||||| ||||||||||||||||||||||| || ||| | |||||||| || |||
------------gtacgctttggattctgctggtctgaattt---tttgggggtatttctgtacaaattatacgctaattatgtattctgcatacctcta-tacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTCATG

upper sequence: GLYMA05G26630.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 8
gtctgtattctgttttactaagaaatttttctgtatttatct-gctcttcacctcactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG
           ||    ||   | |||   |   | ||| |  | |||| |  |  |   ||      | ||||||        | ||  || | |    | ||||||||||||| ||||| |||||||||||| |||| ||||| ||||||||| | |||
-----------gtgaaccttgaatattaaaccaaagttaccccgatctttaaattccgtttcttggatccttaccccc------tttatgtgttgtacgaattgcagGTTGGCTACGTGACAACCATATGCTTTACATGTTTCCTCATCAGATGTATCATG

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|51334723|gb|CO978589.1|CO978589
EST:     TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG                         GTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
genomic: TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAGgtctgtattc ... tctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
EST: gi|193718027|gb|FK653803.1|FK653803
EST:     TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG                         GTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
genomic: TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAGgtctgtattc ... tctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
EST: gi|151402287|gb|EV272100.1|EV272100
EST:     TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG                         GTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
genomic: TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAGgtctgtattc ... tctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
EST: gi|151407580|gb|EV277395.1|EV277395
EST:     TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG                         GTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
genomic: TGCAACGCTTTCCTGTGGAATCCAAAGGTCGACGCAAGAAGCTACAAGAGgtctgtattc ... tctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
EST: gi|254327808|gb|GR834773.1|GR834773
EST:     ATCCAAAGGTCGACGCAAGAAGCTACAAGAG                         GTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT
genomic: ATCCAAAGGTCGACGCAAGAAGCTACAAGAGgtctgtattc ... tctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG
                                            ttctaat  putative branch site (score: 2)
                                         tctttct  CT-rich tract
                            ttaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtattctgttttactaagaaatttttctgtatttatctgctcttcacctcactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG