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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcatttgtcccttttaagttataaattatccttattaattcctttccctttgtactctttaattttgatacttttcttttttacatgttttttctctgtaatacttttgtagttcttttaatcaaataaattgattctgaatgttgacaatgtaattttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAGATCAGGAGTTACCTTGACCTTGTTATTGATGGAAAGCTTCCATTAAACC

Basic information

species Glycine max
transcript GLYMA11G34980.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttcatttgtcccttttaagttataaattatccttattaattcctttccctttgtactctttaattttgat-----acttttcttttttacatgttttttctctgtaatact-tttgtagttcttttaatcaaataaattgattc-tgaatgttgacaatgtaattttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAGATCAGGAGTTACCTTGACCTTGTTATTGATGGAAAGCTTCCATTAAACC
       || |    ||||   || |    ||  | ||||  | |        |||    |  |||  ||||     |||| |    |||  ||   | |||| || ||   |  || | |   |  || |    |         | | |||      |  ||| |||     |||| | ||||||||| || ||||||||||| ||||||||| | |||   |||||| ||||||| ||||||||||| || || |||||||| ||  ||||||
------gttcttgtctttacaatacatgaaattttcattatcttcccattaaatgtctgttgaaatcatgatgggggacttgtaggatttgtattgatgttct-tgcaaggttacttatggacataatagttttctgctcgaggacataaataactttatagtattttgcaccagGTCACTGCAAAACTTACTGCTTTGAAGGGGTTGGATGCACGTCTTCGGGAGATCCGGAGTTATCTTGACCTTGTAATCGAAGGAAAGCTCCCTCTAAACC

upper sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttcatttgtcccttttaagttataaattatccttattaattcctttccctttgtactctttaattttgatacttttcttttttacatgttttttctctgtaatacttttgtagttcttttaatcaaataaattgattctgaatgttgacaatgtaattttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAGATCAGGAGTTACCTTGACCTTGTTATTGATGGAAAGCTTCCATTAAACC
         ||   |||    | | | || |      ||||    ||   | |    ||  ||||| || || |   || |  ||      ||  ||||   |  |  | ||  |  | | || |  |  ||| |||   |   |||  ||  |||| ||      |||| | ||| ||||| || ||| ||||||| ||||||||| |||||   |||||| ||| ||||||||||||||| || || ||||| || ||||||||||
---------gttattttc--ttcacacataac-----ttaaacatttcatcatcaagcttcttaatgtttattcaaatcatgattg-----ttgctctcaaaacaaaatgtgaggaacatata-ttgaggaaactgaaattatttgtgaac--tgtatttc-----agGTCACTGCGAAACTTACTGCTCTGAAGGGATTGGATGCACGACTTCGGGAGATCCGGACTTACCTTGACCTTGTAATCGAAGGAAAACTCCCATTAAACC
















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|254323156|gb|GR835764.1|GR835764
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|208217759|gb|GE016057.1|GE016057
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|6071648|gb|AW101035.1|AW101035
EST:     CTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTTGCA-CAGAG                         GTAAGTGCAAAACTCACAGCTTTTGAAGGG
genomic: CTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTT-GCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTT-GAAGGG
EST: gi|58016090|gb|CX702832.1|CX702832
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|15662128|gb|BI699499.1|BI699499
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATCCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|12774685|gb|BG239612.1|BG239612
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|193630911|gb|FK585066.1|FK585066
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGGTTTGGATGCAAGACTTAAAGA
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGG-TTTGGATGCAAGACTTAAAGA
EST: gi|207802987|gb|GD773500.1|GD773500
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|254323157|gb|GR835765.1|GR835765
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|58017218|gb|CX703960.1|CX703960
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|208073938|gb|GD867771.1|GD867771
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|5058103|gb|AI736579.1|AI736579
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|9902080|gb|BE611048.1|BE611048
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|208099388|gb|GD898833.1|GD898833
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|58017413|gb|CX704155.1|CX704155
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|58023179|gb|CX709920.1|CX709920
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|207740941|gb|GD714319.1|GD714319
EST:     ATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
EST: gi|151411180|gb|EV280991.1|EV280991
EST:     ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAG                         GTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG
genomic: ACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTGCAACAGAGgtttcatttg ... ttttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcttttaatcaaataaattgattctgaatgttgacaatgtaattttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAGATCAGGAGTTACCTTGACCTTGTTATTGATGGAAAGCTTCCATTAAACC
                               tgttgac  putative branch site (score: 3)
     ttttaatcaaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcatttgtcccttttaagttataaattatccttattaattcctttccctttgtactctttaattttgatacttttcttttttacatgttttttctctgtaatacttttgtagttcttttaatcaaataaattgattctgaatgttgacaatgtaattttacatagGTAAGTGCAAAACTCACAGCTTTGAAGGGTTTGGATGCAAGACTTAAAGAGATCAGGAGTTACCTTGACCTTGTTATTGATGGAAAGCTTCCATTAAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA