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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATCAAATATGGGGGTTTTGGGCAAAGAAGCTTTGGCCGCAATGACTGCCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatatttgtctagctgggtgatttgggccacttggttattttttgttagtcttgaaatttcctgttgtgtttcctgatacttttcgacttaactgaag

Basic information

species Zea mays
transcript GRMZM2G123624_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 5'ss of exon 6
GAAATCAAATATGGGGGTTTTGGGCAAAGAAGCTTTGGCCGCAATGACTGCCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatatttgtctagctgggtgatttgggccacttggtta-ttttttgttagtcttgaaatttcctgttgtgtttcctgatacttttcgacttaactgaag
 || ||||| ||||||||| | ||||| |||||  | ||  |||||||||| |||||||  |||||||||||||||||  |||| || || |||||| ||||| || | | |   ||| | | | || ||||| ||| ||| ||  ||||| | ||||| |  |    ||   || | ||| |||  | |||||| ||||||
AAAGTCAAACATGGGGGTTCTAGGCAAGGAAGCCGTTGCATCAATGACTGCTGTTGAAGCTCAACAGCAAAGACTGACCTTGCAACGACTAATTGCAATGgtatat-tctat---gcttgtttagtttggccaattgattagttccttgtttgccttgagaaataaaatttctttacatgacactact-gactta-ctgaag
















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|60398124|gb|DN230940.1|DN230940
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|28985206|gb|BQ539380.2|BQ539380
EST:     CAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|78545157|gb|DV622655.1|DV622655
EST:     CCG-TGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|32919380|gb|CF024192.1|CF024192
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|71768413|gb|DR966350.1|DR966350
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|76935690|gb|DV174431.1|DV174431
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|149085095|gb|EE174602.2|EE174602
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTAC
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTAC
EST: gi|71765024|gb|DR962961.1|DR962961
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAAATCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|74239023|gb|DT646937.1|DT646937
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|71768414|gb|DR966351.1|DR966351
EST:     CCGTTGNAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCCAAAAGGTCCTACAAATTTCTTGATC
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACC-AAAAGGTCCTACAAATT-CTTGATC
EST: gi|71434707|gb|DR815757.1|DR815757
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GGTGAATCAGAGAGAAACTACCACCAAA-GGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|78074542|gb|DV502976.1|DV502976
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|20506722|gb|BQ279315.1|BQ279315
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAG
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAG
EST: gi|76019273|gb|DT946443.1|DT946443
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|60358710|gb|DN225683.1|DN225683
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|71328410|gb|DR800842.1|DR800842
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         NTTGAATCAGAGAGAAACTACCACCAAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAA
EST: gi|74244904|gb|DT652818.1|DT652818
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTA
EST: gi|211409238|gb|FL441029.1|FL441029
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|71765023|gb|DR962960.1|DR962960
EST:     AAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: AAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|71756340|gb|DR954277.1|DR954277
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|149085094|gb|EE174601.2|EE174601
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|71328409|gb|DR800841.1|DR800841
EST:     CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA

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), 46 (downstream exon)
Score: 143

GAAATCAAATATGGGGGTTTTGGGCAAAGAAGCTTTGGCCGCAATGACTGCCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 81

GAAATCAAATATGGGGGTTTTGGGCAAAGAAGCTTTGGCCGCAATGACTGCCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 56

GAAATCAAATATGGGGGTTTTGGGCAAAGAAGCTTTGGCCGCAATGACTGCCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 61

GAAATCAAATATGGGGGTTTTGGGCAAAGAAGCTTTGGCCGCAATGACTGCCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatattt ... ttaactgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATCAAATATGGGGGTTTTGGGCAAAGAAGCTTTGGCCGCAATGACTGCCGTTGAAGGCCAACAGCAAAGACTGACACTGCAGCGTCTTATTGCATTGgtacatatttgtctagctgggtgatttgggccacttggttattttttgttagtcttgaaatttcctgttgtgtttcctgatacttttcgacttaactgaag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG