Skip to another splice site:
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 5'  3'   		10  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgataggttccccgacttttttttttcccatggcccgcccatatacacgttgctaaccgactgggtgtgtgtggttcttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG

Basic information

species Zea mays
transcript GRMZM2G146463_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146463_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g26900.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------------gtaagtgataggttccccgacttttttttttcccatggcccgcccatatacacgttgctaaccgactgggtgtgtgtggttcttgcga-tagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG
                                                              |   | ||      | |||| | | |  |     | | ||   | | |      |||     |  ||   |||  || |     |||  |||||||||  ||||||||||   |||||||||| |||| | |||||||||||||||||||||||||
gtaaaccgccgccgccgccgcgagccgctggccctctgctccggccggcgaccgatttcggttgcattatgctgatcgcgacatgtgtgatgtgtcttgtcctttcctttgatttctgc-gtttgtttgccggtgattgatgtaatcgagcagCATGCTGAGCAACATCGACAGCAACGACGCCTCCGCCAGCTACGCCAAGCCCGGCGGCTGGAACG
















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|22935898|gb|BU572173.1|BU572173
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|78108215|gb|DV526633.1|DV526633
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|86465787|gb|DY232160.1|DY232160
EST:     CGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: CGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|78113278|gb|DV531670.1|DV531670
EST:     CAACGACCCATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: CAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|86466262|gb|DY232634.1|DY232634
EST:     ACGGC-ACAGCCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: ACGGCAACAG-CTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|22472587|gb|BU037067.1|BU037067
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTA
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTA
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCCGTACGCCCAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|26560002|gb|CA832237.1|CA832237
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCCAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|71443417|gb|DR824467.1|DR824467
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|50334851|gb|CO529977.1|CO529977
EST:     ACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: ACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|60357458|gb|DN224431.1|DN224431
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAAC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAAC
EST: gi|87157241|gb|DY402030.1|DY402030
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACG
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACG
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCNAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCNAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAAC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAAC
EST: gi|23199550|gb|BU582115.1|BU582115
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACTACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|26559550|gb|CA831785.1|CA831785
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     ACNGGCA-CAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACCCCCAAGC
genomic: AC-GGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCC-AAGC
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|87156914|gb|DY401703.1|DY401703
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCCTGA-CGACGCCTACGCCCGGGACGCCAAGC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACC-TGAACGACGCCTACGCCCGGTACGCCAAGC
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|78088430|gb|DV516823.1|DV516823
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGGACGCCTAGCC
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCC
EST: gi|76930345|gb|DV172346.1|DV172346
EST:     TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG                         CATGCTGGGACA-CATCGACCT
genomic: TACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGG-ACAACATCGACCT

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), 49 (downstream exon)
Score: 41

GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 32

GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 12

GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG


Block sizes: 37 (upstream exon), 44 (downstream exon)
Score: 4

GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGGgtaagtgata ... cttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcccgcccatatacacgttgctaaccgactgggtgtgtgtggttcttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG
                   tgctaac  putative branch site (score: 4)
                                           ttcttgc  putative PPT
         atataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgataggttccccgacttttttttttcccatggcccgcccatatacacgttgctaaccgactgggtgtgtgtggttcttgcgatagCATGCTGGACAACATCGACCTGAACGACGCCTACGCCCGGTACGCCAAGCCCGGCGGCTGGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA