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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattttcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt...

Basic information

species Zea mays
transcript GRMZM2G000393_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g07905.2 (Oryza sativa), 5'ss of exon 9
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattttcctgttaggagatactacctcccgttcacaaata--tatgacactgttgattt
||| |||||||||||||||||||| |||||||| ||||||||||||||||||||||| || |  ||| |||    ||      ||| || |||| ||  |  | ||      || |       | | |  ||||  | ||   ||  || | |
GGGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaactaacatattcaaggtccttgccatttgtctatt-atcctaatattcatct-tagtgttgggtgattagcaataattctgtgtctagtggtgt

upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA14G14000.1 (Glycine max), 5'ss of exon 9
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcat-----tctcctgaattagtttatt-cattttcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt
|||  | | ||||||||||||||| |||||||||||||| |||  |||| ||| ||| |  | || | | | |       | |  ||| ||| ||||||  ||| | |||  | ||  | | |  |     ||  ||||  ||  || |        
GGGAAAGCCATGGTATGAACCTGATTGGTGGAAATTTGGGGATGAAAAATCgtaagtaatataccttttgcacgagatgatttggtgatttattttattatattatactggaatgatcttcgatgttatcgtcttaaattgataccatttc------

upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT4G32120.1 (Arabidopsis thaliana), 5'ss of exon 9
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattt----tcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt
|||    ||||||||||| |||||||||||||||||||| ||    ||| ||| |||    ||  | ||  |   ||| ||   |||  | |  |  ||     | |  | |    ||||   |  | ||     || |||              
GGGAAGTCAATGGTATGAGCCTGAGTGGTGGAAATTTGGGGACGACAAATCgtaagt-gtcttatacctcataggtcttctcgtttatgtcaagcccttgtgaccttcgttgtgtgtactcagtttctttgttcgatttatttag----------

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|32928477|gb|CF033289.1|CF033289
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|32846895|gb|CD986576.1|CD986576
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAACTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTTTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|211130920|gb|FL136658.1|FL136658
EST:     GCCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: G-CCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTC-ACCTC                         G
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacag-
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTC-ACCTC                         G
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacag-
EST: gi|74246238|gb|DT654152.1|DT654152
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|32929367|gb|CF034179.1|CF034179
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGGTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|149005473|gb|EE040028.2|EE040028
EST:     GGCCACCAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTTTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|24765385|gb|CA400544.1|CA400544
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|50323552|gb|CO518678.1|CO518678
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|5124017|gb|AI745858.1|AI745858
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|21828587|gb|BQ703271.1|BQ703271
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|110200892|gb|EC882789.1|EC882789
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|15082759|gb|BI389443.1|BI389443
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|113703856|gb|EE681360.1|EE681360
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC

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: 90

GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 141

GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 120

GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattttcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt

- - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - -  GGAGAT