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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaagaaaacttattcttgaaatacttaactaagactacaaggacccagttattcatgacacctctcatgtttctcacacataattaagtaatagaaaaaaactggactattaacggatttcaggctggtcgctggctgagctcttgctccttgtttacag

Basic information

species Zea mays
transcript GRMZM2G365035_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G365035_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g22710.4 (Oryza sativa), 5'ss of exon 8
GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtat-cttaagaaaacttattcttgaaatacttaactaagactacaaggacccagttattcatg-acacctctcatgtttctcacacataattaagtaatagaaaaaaactgga--ctattaacggatttcaggctggtcgctggctgagctcttgctccttgtttacag
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| |||||| |||||||||| |||||||||  | |    |||  ||    ||||| | |   ||    |||     ||      ||| ||  |   |    | | |||  |  | |||||     |||| | || |  | |   |||| |   | |||| |||  ||  |   ||   |||| |   |||| | |||
GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACGGAGATGGCTATATCACATCTGATGAACTGAGAATGgtacacctcttcaaa--tacctgtgaaacattactcttttcctattc--acgtgagaattgatttatttcctataagattccaatccttaattggtgcatagcataagatcgtaatttattcaaccagttcatgcttctca-tatatgtattcttaca--ttgtctgcag
















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|149087834|gb|EE287144.2|EE287144
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTTTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|211142539|gb|FL467000.1|FL467000
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|18649798|gb|BM498617.1|BM498617
EST:     AGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|76017952|gb|DT945122.1|DT945122
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|149043308|gb|EE047371.2|EE047371
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTTTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|60345110|gb|DN212083.1|DN212083
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|4688566|gb|AI637236.1|AI637236
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACANT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|22489585|gb|BU049508.1|BU049508
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|76284446|gb|DV024014.1|DV024014
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTTTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|87153749|gb|DY398538.1|DY398538
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|61118774|gb|DN559735.1|DN559735
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|166632170|gb|EG309972.1|EG309972
EST:     CTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: CTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|32935092|gb|CF039904.1|CF039904
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGGTGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|18384244|gb|BM417443.1|BM417443
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|37388728|gb|CF631576.1|CF631576
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|33091766|gb|CF051760.1|CF051760
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|22489749|gb|BU049672.1|BU049672
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|32840607|gb|CD980288.1|CD980288
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|45567561|gb|CK985631.1|CK985631
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|113701806|gb|EE679310.1|EE679310
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTTTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|12058142|gb|BF727762.2|BF727762
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|149102041|gb|EE188040.2|EE188040
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTTTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|6696017|gb|AW289125.1|AW289125
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT

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: 46 (upstream exon), 49 (downstream exon)
Score: 39

GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 104

GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 55

GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACATGATACTGAGAAGTGGAAATCATTGTCTCAAGCTGCATTTGATAAATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaagaaaacttattcttgaaatacttaactaagactacaaggacccagttattcatgacacctctcatgtttctcacacataattaagtaatagaaaaaaactggactattaacggatttcaggctggtcgctggctgagctcttgctccttgtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG