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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctttgaatatttcagcatcagcatattttctatgctagaagacaccttatgtatgttttattttgctttggtgtgattgtggtgataatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG

Basic information

species Glycine max
transcript GLYMA06G48060.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g48990.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------aatctttgaatatttcagcatcagcatattttctatgctagaagacaccttatgtatgttttattttgctttggtgtg-attgtggtga----taatgttt-------gaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
                                            |   ||  ||   |    |  || |   | |  ||   |  |    | |     ||  |||  ||| ||      || ||  || |      |||   ||        |||||||||||||||   ||||| || || ||  ||||||||||||| || || || ||||| ||||| |||||||| ||||| ||||| || |||   ||||
gtaaagacactgtctattctttgagttgatctgaaaactgtactacactttgatgcatttttactaggactctatggatatgaacaattgcttcccacataattt-ctttactacaacatgtatactgattgcatctaactcttctctgttaaagGATTTTGAATTTCATGAGCTAGAGGAGGTGCTGCAGTATTATCCCCATGGTTATCATGGTGTTGACAAGGAAGGAAGGCCCGTCTATATCGAGTTGCTTG

upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G459982_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------aatctttgaatatttca--gcatcagcatattttctatg--ctagaagacaccttat-gtatgtttt------attttgctttgg--tgtgattgtggtg----ataatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
                                              | |||    |||| |    | ||   |||    ||||||   |  ||||    | ||  |||| |||      | | |||  ||   | | |  || |       || |  ||||||||||||||||||   || || || || ||  |||| ||||||||||| || |||||||| ||||| |||||||| ||||| ||||||||||||   ||||
gtaggatgttgtctactctagaaagttgatctcaaagttatatgaaactctgctgatatatagatgtatttacatgcactctatggcttctaagattgttcatcatatgattttgcaaaactatgccatgccttttaacagtagcttactgtactcgttgaagGATTTTGAATTTCATGAACTAGAGGAGGTCCTGCAATATTATCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTCTACATTGAGTTGCTTG

upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G452580_T03 (Zea mays), 3'ss of exon 4
----------------------------------------------aatctttgaatatttca--gcatcagcatattttctatg--ctagaagacaccttat-gtatg-ttttattttgctttggtgtg-attgtggtgataatgt----------ttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
                                              | |||    |||| |    | ||   |||    ||||||   |  ||||    | ||  |||| || |      || ||   || ||  |     ||   |          ||||||||||||||||||   || || || || ||  |||| ||||||||||| || |||||||| ||||| |||||||| ||||| ||||||||||||   ||||
gtaggatgttgtctactctaaaaagttgatctcaaagttatatgaaactctgctgatatatagatgtatttacatgcactctatggcttctaagattgttcatcatatgattctgcaaaactatgtcatgcatattaacagtagcttactgtactcgttgaagGATTTTGAATTTCATGAACTAGAGGAGGTCCTGCAATATTATCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTCTACATTGAGTTGCTTG

upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G014994_T03 (Zea mays), 3'ss of exon 3
---------------------------aatctttgaatatttcagcat-----cagcatattttc-tatgctagaagacaccttat-gtatgtttt------attttgctttg-gtg-tgattgtggtga----taatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
                            ||||   ||| ||     |          |||||  | ||| | | ||||    | ||  |||| ||       | | ||   ||  |  | |  || |  |     | |  ||||||||||||||||||   ||||| || || ||  |||||||||| ||||| || |||||||| ||||| |||||||| ||||| || |||||||||   ||||
gtaggatgttgtctattctaaaaagttgatctcaaaatcttatgaaactctgctgatatattgacgtatacgataagattattcatcatatgcttctgcaaaactatgtcatgcatactaacagtagctaacttcactcattgaagGATTTTGAATTTCATGAGCTAGAGGAGGTCCTGCAGTATTACCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTGTACATTGAGTTGCTTG

upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------------aatct-ttgaatatttcagcatcagcatattttctatgctagaagacaccttatgtatgttttattttgctttggtgtgattgtggtgataatgtttga-agGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
                                                                        ||  |  |   |||||       ||||| |  || || ||       |  | ||| |     ||| |  || |  |    ||    ||    ||  ||  |||||||||| || | |||||| |||||||| ||||| || ||||||||||| || |||||||||||||||||||| || || ||||||||||| |||||||
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatc-attctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG

upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G56160.1 (Arabidopsis thaliana), 3'ss of exon 4
aatctttgaatatttcagcatcagcatattttctatgctagaagacaccttatgtatgttttattttgctttggtgtgattgtggtgataatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
      |      |   |  |||||     ||  |   ||| ||   | |  |||     | |      |||             ||||||  |    |||||||  | ||   |||| |||| |||||      | | |||||||||||||| |||||||||||||| || || || ||  | || || ||||||||||
-----gtacgagatatggtttcagctgtggtttcagagtagtagcatcttgctgtggaactaacaacatttta-------caaattgataaaat----agGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG

upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 4
---aatctttgaatatttcagcatcagcatattttctatgctagaagacacc-ttatgtatgttttattttgctttggtgtgattgtggtgataatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
        |||  | ||  |    ||    ||  | ||||  | | |      || | |     |||| |||| |     | |   ||   |       ||||||| ||||||||   ||||||||| || || || || || || |||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||
tactgctcttggcttttcta----caatggatgatttatgagaaatgtttttgttttctgaacattatattgcctaatcctaacactgtataatcgaaatgaagGACTTTGAATTCAAAGAGCTGGAGGATGTCTTACAATACTACCCTCAAGGATACCATGGAGTTGATAAGGAAGGAAGGCCAGTTTACATTGAGAGACTTG

upper sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
aatctttgaatatttcagcatcagcatatttt---ctatgctagaagacaccttatgtatgttt-tattttgctt-tggtgtgattgtggtgata-atgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
      |   |  |||  || ||| | ||  |    ||||  ||  | ||  |  ||| | ||| |||   | || |  |  |   || |||||   |   |  |||| ||  |||||  |||  | ||  ||||   | | || |||||||||||||| ||||| || ||||| ||||| ||||| || |||||||| ||| |||
------tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG

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|193301969|gb|FK266510.1|FK266510
EST:     TTGGCGAAAGGAATATGGAACTGATACCATCCTTGAG                         GATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTAATTATCCTCAAGG
genomic: TTGGCGAAAGGAATATGGAACTGATACCATCCTTGAGgtataaagat ... atgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGT-ATTATCCTCAAGG
EST: gi|208209891|gb|GE006416.1|GE006416
EST:     AAGAAATGCTTACTTGGCGAAAGGAATATGGAACTGATACCATCCTTGAG                         GATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGG
genomic: AAGAAATGCTTACTTGGCGAAAGGAATATGGAACTGATACCATCCTTGAGgtataaagat ... atgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccttatgtatgttttattttgctttggtgtgattgtggtgataatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
     tatgtatgttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctttgaatatttcagcatcagcatattttctatgctagaagacaccttatgtatgttttattttgctttggtgtgattgtggtgataatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - catcagc
- - - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - -ccttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg