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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgatgtttggcccagctaatactggatttggagccaactgtattttatgtctatactcacgtatccttgcccgtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG

Basic information

species Zea mays
transcript GRMZM2G105019_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 9
-------------------------------gtacgtgatgtttggcccagctaatactgg-atttggagccaact-gtattttatgtctatactcacgtatccttgcccgtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG
                               ||   | |    || ||  ||| | |   |    |  ||  |  | | | ||| | |   ||  ||   | |  ||  | | | ||||||| ||||| || || |||||||| || ||||||||||||||||||||  | ||||||||||| || ||||| |||||||| |||||||| ||||| ||||
gtatgtctttctttagcacaattgatgaaatgtttataactagtgaccttgctgacagaagtgcgtttagtaagtttgaactttgtatacttatacat-caacgatgtgcttgtttgcagGTTGAATCTAACGGTACTGTTCTGTCGACCAATTGGAAAGATGTTGGCTCGAAGAAGGTAGAGGGAAGCCCACCTGATGGGATGGAGCTTAAGAAATGGG
















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|148972746|gb|EE023715.2|EE023715
EST:     TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|211436238|gb|FL480984.1|FL480984
EST:     TCTACAAGGATGCTGATGAAGATATGCGGAGGCCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|40337441|gb|CK371511.1|CK371511
EST:     TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|166691075|gb|EG165850.1|EG165850
EST:     ATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAG
genomic: ATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAG
EST: gi|8383133|gb|BE056076.1|BE056076
EST:     TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|166552843|gb|EG168280.1|EG168280
EST:     AGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: AGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|166512918|gb|EG157470.1|EG157470
EST:     TGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: TGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|6031470|gb|AW076372.1|AW076372
EST:     TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|32857112|gb|CD996793.1|CD996793
EST:     TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
genomic: TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|13558772|gb|BG550127.1|BG550127
EST:     AAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTCTCAGCCAATTGGAAAGATGTTGGAGCA
genomic: AAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCA
EST: gi|166539784|gb|EG136998.1|EG136998
EST:     TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTC                         GTGGAATCAAATGGCACTGTTCTC
genomic: TCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 319

GGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 404

GGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

GGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

GGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGTCATTCgtacgtgatg ... gtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggagccaactgtattttatgtctatactcacgtatccttgcccgtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG
                          tactcac  putative branch site (score: 118)
                                    tccttgcccgtttct  putative PPT
             tattttatgtctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgatgtttggcccagctaatactggatttggagccaactgtattttatgtctatactcacgtatccttgcccgtttctgcagGTGGAATCAAATGGCACTGTTCTCTCAACCAATTGGAAAGATGTTGGAGCAAAGAAGGTAGAAGGGAGCCCCCCTGATGGTATGGAGCTCAAGAAGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT