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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actacatcatccaacttgaggcttatgcttttttctagttaatgttttatattccaattttgaaaaccttttaacagaatatacatgcattccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG

Basic information

species Glycine max
transcript GLYMA20G28420.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28420.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------------------------------actacatc----atccaacttgaggcttatgcttttttctagttaatgttttatattccaattt-tgaaaaccttttaacagaatatacatgcattccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG-----
                                                                                | | ||||     |  ||| | ||  | |  ||||  | |   |   |||       | ||    |    |  |  || | ||   | | |    |            |||||||||| ||||| || || ||||||||||||||||| |||||||| |||||| | || ||||||||||||||||| |||||    || || ||     
gtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCA

upper sequence: GLYMA20G28420.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094255_T02 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------------------------actacatcatccaacttgaggcttatgcttttttctagttaatgttttatattccaattttgaaaa-------ccttttaacagaatatacatgcattccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG-----
                                                                                         | |   |     | | | ||||  |     ||   |  |   | |||| |||  | | |||| |         || | | ||   || |   | ||| |  |||    | |||||||||||||||| || || ||||| || |||||| | |||||||| ||||||||||| |||||||| |||||||||||||| |  || || |      
gtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttga-agCTTGCTGGGAAAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCA

upper sequence: GLYMA20G28420.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 6
--------actacatcatccaacttgaggcttatgcttttttctagttaatgttttatattccaatt-ttga-aaaccttt--taacagaatatacatgcattccctctgagCA---CAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG-----
        | | ||  |||   ||| | || || |         |   || |||  || || ||  | |||| ||||||||  | | |  || |  || |||| |   | |  |   ||||||||||| ||||| || ||||| || || || || ||||| || || |||||  | ||||| |||||||||||||||| ||||||||| ||| |     
gtattaggattcca--atctttcttaaagcatacgaggacaataacagaacgtta-atgtttcatctgttgacaaacctttcttgataagatttg-attcatttctatttattatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGA

upper sequence: GLYMA20G28420.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 6
-actacatcatccaacttgaggcttatgcttttttctagttaatgttttatattccaattttgaaaaccttttaacagaatatacatgcattccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG-----
 | |   |     |  | |   ||||  |   |||   |  |   ||   || ||   |||  | |    ||| |||||| ||   | || |     |||    |||||||||| ||||||||||||||||||||||||||||| ||||| ||||| |||   ||||||||||||||    || ||||| ||||| || |      
taatgatttccttaggtagcaacttaaacggatttactgaaatatttccgtagtc---tttctacacaagtttgacagaaaat---ttcaatgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA

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|209713507|gb|BW679284.1|BW679284
EST:     CACGTCTGGTATGACACTTCACATT---CAG                         --CAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: CACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|192295567|gb|FG988141.1|FG988141
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG                         C-----TTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|254323948|gb|GR836180.1|GR836180
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG                         C-----TTGCTGGGAAAAATTCTCATCATATTATT
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATT
EST: gi|192298863|gb|FG987608.1|FG987608
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG                         C-----TTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|16278546|gb|BI942961.1|BI942961
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATT---CAG                         --CAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|58021912|gb|CX708653.1|CX708653
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATT---CAG                         --CAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|16105448|gb|BI893188.1|BI893188
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATT---CAG                         --CAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|120528942|gb|EH257076.1|EH257076
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATT---CAG                         --CAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|120496152|gb|EH224319.1|EH224319
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG                         C-----TTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
EST: gi|16278135|gb|BI942744.1|BI942744
EST:     TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG                         C-----TTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG
genomic: TCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAGgtattaatac ... tccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatattccaattttgaaaaccttttaacagaatatacatgcattccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG
                       ttttaac  putative branch site (score: 2)
                                          cattccctct  putative PPT
                       ttttaacagaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actacatcatccaacttgaggcttatgcttttttctagttaatgttttatattccaattttgaaaaccttttaacagaatatacatgcattccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - tcatcca
- - - - - - - - - - gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgca