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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactcgttccattagtattgcttttcttgcgatggccccttgtcgatcgctacagatgtggaaaatgggtaaaggctagagtttgtgacgtttta...

Basic information

species Zea mays
transcript GRMZM2G000660_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000660_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g02120.2 (Oryza sativa), 5'ss of exon 3
TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgt----actgactcgttccattagtattgcttttcttgcgatggccccttgtcgatcgctacagatgtggaaaatgggtaaaggctagagtttgtgacgtttta
  || |    ||    |    |||||||| |||||||||||||| ||||||||||||||| | |||||||| || |||||||| ||||| || ||| | |||    ||  |    ||   |     |       |||  |||    ||| |   ||   |  |  | ||| |   || |      |  | || ||  ||    |
CTGTGCCGCTCCTCCACGACGGGGAGCACTAGGATGGAGGACTACAACACCGCCATGAAGAGAATGATGCGCAATCCCTACGAATACCACCATGATTTAGgtccgtaccaatcatttttttcctcgtctacgcgcttttgatcctacctagataatgattctatttttgggatggggattg----ttaatttcgtcccgccgaa

upper sequence: GRMZM2G000660_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g02180.1 (Oryza sativa), 5'ss of exon 1
TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgt----actgactcgttccattagtattgcttttcttgcgatggccccttgtcgatcgctacagatgtggaaaatgggtaaaggctagagtttgtgacgtttta---
  || |    ||    |    || ||||  |||||||||||||| ||||||||||||||| | |||||||| || |||||||| ||||| |||||| | |||    ||  |    ||    | ||||      | |||  |||   ||| |   ||   | ||  |  |||   |||| |  |  |  | || ||  ||    |   
CTGTGCCGCTCCTCCACGACGGGAAGCAGTAGGATGGAGGACTACAACACCGCCATGAAGAGAATGATGCGCAATCCCTACGAATACCACCACGATTTAGgtccgtaccaatcatttttcctcgtatacgcgcttttg--atgctacctagataatgattccatttcggga---tggggattg--ttaatttcgtcccgccgaaacg
















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|76290166|gb|DV029734.1|DV029734
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|211492252|gb|FL110848.1|FL110848
EST:     GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCCTCG                         GCATGAACTATGCTGTCATAAGTGA
genomic: GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATC-TCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGA
EST: gi|76920052|gb|DV167984.1|DV167984
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|211492253|gb|FL110849.1|FL110849
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|211492251|gb|FL110847.1|FL110847
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|89253115|gb|DY624901.1|DY624901
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|211492250|gb|FL110846.1|FL110846
EST:     GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGAT
genomic: GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCT-CGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGAT
EST: gi|211492254|gb|FL110850.1|FL110850
EST:     GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCT
genomic: GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATC-TCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCT
EST: gi|13198546|gb|BG354375.1|BG354375
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCC
EST: gi|33467334|gb|CF244383.1|CF244383
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|37422589|gb|CF649009.1|CF649009
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|93283004|gb|EB675268.1|EB675268
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|89253066|gb|DY624852.1|DY624852
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|71302332|gb|DR787284.1|DR787284
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|211495128|gb|FL110852.1|FL110852
EST:     GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGANCNTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCT
genomic: GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATC-TCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCT
EST: gi|71311577|gb|DR792164.1|DR792164
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|71312902|gb|DR792973.1|DR792973
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|211492248|gb|FL110844.1|FL110844
EST:     GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGANCNTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCT
genomic: GCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATC-TCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCT
EST: gi|78105236|gb|DV523654.1|DV523654
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|71426637|gb|DR807687.1|DR807687
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|78075798|gb|DV504232.1|DV504232
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|60345940|gb|DN212913.1|DN212913
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
EST: gi|76927038|gb|DV171123.1|DV171123
EST:     CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCG                         GCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC
genomic: CGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTC

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

TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTCAGAAGCCTGAAGATATCGATCGCTTGAAAAATGAAGAGCGAGTAGCATA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 37

TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTCAGAAGCCTGAAGATATCGATCGCTTGAAAAATGAAGAGCGAGTAGCATA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 12

TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTCAGAAGCCTGAAGATATCGATCGCTTGAAAAATGAAGAGCGAGTAGCATA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 79

TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactc ... tggaatacagGCATGAACTATGCTGTCATAAGTGAGAGCTTGATTGTTGGCTCACAGCCTCAGAAGCCTGAAGATATCGATCGCTTGAAAAATGAAGAGCGAGTAGCATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTCCACGGCCGGAGCCCAAGGGAGCACGAGGATGGAGGACTATAACACCGCCATGAAGCGGATGATGCGTAACCCCTACGAGTACCATCACGATCTCGgtactgactcgttccattagtattgcttttcttgcgatggccccttgtcgatcgctacagatgtggaaaatgggtaaaggctagagtttgtgacgtttta

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC