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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagatggttttgatttttgacaacattgattgtgtgctagagcctaggggaaataaaaaacaatttcattgctgcctgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT

Basic information

species Glycine max
transcript GLYMA12G06920.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------------------agagatggttttgatttttgacaacattgattgtgtgctagagcctagggga-aataaaaaacaatttcattgctgcctgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                                                           |    |  |   |||| | |    | |  | ||     ||    || |      || |||  |||| |   |  || ||      | || | |  ||  ||||| | ||| ||| |||| |||||||| || ||||| ||||| || ||| ||||||| |||||||||||||| ||| |    | | ||||||| ||||||
gtatgtgcatttgctattagttgtatgagtgtttcagtcatgttccatgctatagtgctatgcctcatagagattgtgggactcctccactgctcattaacttcttgcaattgatcaaatccaatatgtgtattgact------ccatgtttgctatcagGTTCACAAATAATATCCTCAGCACAGCCCAGCAAGTTTGGTTACGGAAACTGGGAGGAGCAAAGCCTGTTGTCAATCAGGGGGGTAGTGGGATAATTACT

upper sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G839422_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------------------------------agagatggttttgatttttgacaacattgattgtgtgctagagccta-ggggaaataaaaaacaatttcattgctgcctgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                                                                                       |   | |         |  |  | ||   |||   ||  |   ||     ||||  |  |  ||||  |   |         || || | ||  | |||||||| |||||||||||| |||||||| || || || ||||| || ||| ||||||| || |||||||| |||| |||    | | |||| || ||||| 
gtatgtgcatcagtctcttttgttctaatgggaaatatgttcagatatttgtttcacattatactgctagttgcttcatacaagatcacgagttcacagccccttgcccccttccctgttcactgaattttacaatcaaattcatgattattttgtaatttgtattgactccatgttttccattagGTTTACAAACAATGTCCTCAGCACAGCCCAGCAGGTGTGGTTACGGAAAATGGGAGGAGCGAAGCCTGTAGTGACTGAGGGAGGTAGTGGAATAATTACC

upper sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G110063_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------------agagatggttttgatttttgacaacattgattgtgtgctagagcctaggggaaataaaaa--acaatttcattgctgcctgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                                                                            | | | | |  ||     |  |    || | | |   ||  |   || |   ||| |||    ||| ||  ||  ||  |    | | || | ||  | |||||| | |||||||||||| |||||||| || || || |||||||| ||| ||||||| || |||||||| |||| |||    | | |  |||| ||||| 
gtatgttcatgtcttttttttctaactacaaatatgttcatatattcttgttgcatattatgtcgctagttgcttcaaacaagatcatggccccttccc-tgttcagttttcactgaattttacgattaatcaaatccgcaagtttttttttgtattgactcc-atgttttccattagGTTCACAAACAATGTCCTCAGCACAGCACAGCAGGTTTGGTTGCGGAAAATGGGAGGAGCCAAGCCTGTAGTGAGTGAGGGGGATAGGAGGATAATTACA

upper sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 8
agagatggttttgatttttgacaacattgattgtgtgctagagcctaggggaaataaaaaacaatttcattgctgcctgattttctatttcttttac--------tagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
        |||  | |   |    || | |        || |    |    |  |  | | ||| ||| | | |   | ||     |  |  ||| |        |||||| | ||||||||| ||||||||||| |||||||||||||| || ||||| || ||||| || ||||||||||||||  ||||  |||| || ||||||
--------tttctagtgaagttttcaataaaataaaaataaaatgcaaaatattttcagagcaagttcttcgattgttaatccataagatgctttgcatggctgttagGTTCACAAACAATGTACTGAGCACAGCACAACAAGTATGGTTACGCAAATTAGGTGGTGCCAAACCTGTTGTGAATGAGGATGCAAGTGGAATCATTACT

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|23064105|gb|BU578878.1|BU578878
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCATTTTCTCAACAAGTATGGTTGCGAAAAT
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCA-CAGCTCAACAAGTATGGTTGCGAAAAT
EST: gi|31469715|gb|CD411743.1|CD411743
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|23063997|gb|BU578770.1|BU578770
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|193525562|gb|FK478393.1|FK478393
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAGACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|7926340|gb|AW832366.1|AW832366
EST:     GTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: GTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|5760152|gb|AI965515.1|AI965515
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|22930126|gb|BU547265.1|BU547265
EST:     CTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: CTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|10233625|gb|BE802513.1|BE802513
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACACGTATGGCTGCGAAAATA
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|20498706|gb|BQ273636.1|BQ273636
EST:     GGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: GGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|10844370|gb|BF067669.1|BF067669
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
EST: gi|120493132|gb|EH221299.1|EH221299
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggggaaataaaaaacaatttcattgctgcctgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                             gcctgat  putative branch site (score: 4)
                                   ttttctatttctttta  CT-rich tract
      aaataaaaaacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagatggttttgatttttgacaacattgattgtgtgctagagcctaggggaaataaaaaacaatttcattgctgcctgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- -gatggtt
- - - - - - - - - tgacaac
- - - - - - - - - - - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgc