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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttttccatttaatggaaaatggttattactgcatgtttagctagaatattgttgtttttgctaagagtaaaatacattctaggtccttaaact...

Basic information

species Zea mays
transcript GRMZM2G010146_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010146_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g33020.1 (Oryza sativa), 5'ss of exon 3
CAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttttccatttaatggaaaatggttattactgcatgtttagctagaatattgttgtttttgctaagagtaaaatacattctaggtccttaaact----
|||||||||||||||| || ||| |||| ||||||||||||||||||||||||||||| ||||||||||||||| |||| |||||||| |||||||||||||||| |||  |     |||| ||| | | | | ||     | ||    | |  |||   | | | ||||  || |  ||    ||      |  ||       
CAAGGACTGGTGATCAACGTGACACGCTGAAGCATATCTACAACCTATATGTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttccctgcg-aatgaaaatttgct-tcacccttcggttcataacagcatta--gatatagctatcaggattatctcatcagaaaacaaaatgcatta
















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|71425314|gb|DR806606.1|DR806606
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTG
EST: gi|211038848|gb|FL245344.1|FL245344
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|71302504|gb|DR787370.1|DR787370
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|93284352|gb|EB676616.1|EB676616
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAA-CATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|91872814|gb|EB402771.1|EB402771
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|211038853|gb|FL245349.1|FL245349
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|78083968|gb|DV512361.1|DV512361
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCCA                         GTGCGAACTTTTTCA-CAAACATCTCGATCAATACGTGAGAACAATAATTT
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTT-CAACAAACATCTCGATCAATACGTGAGAACAATAATTT
EST: gi|94477699|gb|EB706657.1|EB706657
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATNCA-TACGTGAGAACAATAATTT
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGAT-CAATACGTGAGAACAATAATTT
EST: gi|76292671|gb|DV032239.1|DV032239
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|148930227|gb|EC872669.2|EC872669
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|71302502|gb|DR787369.1|DR787369
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|76930391|gb|DV172363.1|DV172363
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|71316462|gb|DR794908.1|DR794908
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|78118287|gb|DV536673.1|DV536673
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|71436637|gb|DR817687.1|DR817687
EST:     GGGAATACGTTGTAAAAAATCCTCTGTATGGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATC
genomic: TGGAATACGTTGTAAAAAATCCTCTGTATG-CTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATC
EST: gi|211038850|gb|FL245346.1|FL245346
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|101393644|gb|EB818754.1|EB818754
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|148932965|gb|EE285816.2|EE285816
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|71434336|gb|DR815386.1|DR815386
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|76930392|gb|DV172364.1|DV172364
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|71436488|gb|DR817538.1|DR817538
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|76918988|gb|DV167546.1|DV167546
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|211038851|gb|FL245347.1|FL245347
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|211038847|gb|FL245343.1|FL245343
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|14243987|gb|BG841705.2|BG841705
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
EST: gi|148944695|gb|EC889832.2|EC889832
EST:     GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAA                         GTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG
genomic: GTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTG

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: 39 (upstream exon), 47 (downstream exon)
Score: 48

CAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 64

CAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 60

CAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 52

CAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttt ... ttatttgtagGTGCGAACTTTTCAACAAACATCTCGATCAATACGTGAGAACAATAATTTGATGTCATTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATGCTCCTGGAACACCAATCAAgtaagttttttccatttaatggaaaatggttattactgcatgtttagctagaatattgttgtttttgctaagagtaaaatacattctaggtccttaaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataca