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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtccacaaatcctgatcagtgatcacatatttagataattaatacttcatatccagagtttcttttccattttaaataatgattggtgctaatattatttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT

Basic information

species Zea mays
transcript GRMZM2G353213_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G353213_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 9
gtacgtccacaaatcctgatcagtgatcacatatttagataattaatacttcatatccagagtttcttttccattttaaataatgattggtgctaatattatttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
||| |  |  |  | ||  | |    ||  ||||| | ||||  ||||    || | | ||           ||  | |  | ||||   ||  ||| |||| || | ||||||||||||||||||||||||||||||||||||||||||||||||
gtatgctcctacttactttttaacactccgatatt-acataa--aatat---atgttctga----------tatagtgaggactgatgtctggaaatcttatgttac-agGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT

upper sequence: GRMZM2G353213_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 9
gtacgtccacaaatcctgatcagtgatcacatatttagataattaatacttcatatccagagtttcttttccattttaaataatgattggt--gctaatattatttttc-tagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
       ||    | ||  | | |    | ||||     |||||  ||| | | |||   |  |  ||   || |     |||   ||| |   ||  |  |  ||||  ||||||||||||||||||||  |||||| ||||||||  | || |||||
-----gtcatgttttctt-tgaattggtagatat-----taatttctacatgacatcttaatataattggtcaat--gggtaacagttgcttaactgttgctgcttttaatagGGATGCTGCAGAATCCACAGTACCGTCAACAACTTGAAGAAATGCT

upper sequence: GRMZM2G353213_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 12
gtacgtccacaaatcctgatcagtgatcacatatttagataattaatacttcatatccagagtttcttttccattttaaataatgattg--gtgctaatattatttttc-tagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
       ||    | ||    | || | | ||       |||||  ||| | | |||   | | |  ||  |    |   ||||  ||   || ||  |  |  ||||  ||||||||||||||||||||  |||||| ||||||||  | || |||||
-----gtcatgttttctttgaattggtaatat-------taatttctacatgacatctttaatataattggc-caatgggtaatagtttctgtactgttgctgcttttaatagGGATGCTGCAGAATCCACAGTACCGTCAACAACTTGAAGAAATGCT

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|32789084|gb|CD941320.1|CD941320
EST:     CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGT                         GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
genomic: CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
EST: gi|32803778|gb|CD956014.1|CD956014
EST:     CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGT                         GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
genomic: CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
EST: gi|32800822|gb|CD953058.1|CD953058
EST:     CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGT                         GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
genomic: CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
EST: gi|32803516|gb|CD955752.1|CD955752
EST:     CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGT                         GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
genomic: CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
EST: gi|32803636|gb|CD955872.1|CD955872
EST:     CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGT                         GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
genomic: CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
EST: gi|32803661|gb|CD955897.1|CD955897
EST:     CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGT                         GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
genomic: CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
EST: gi|32803435|gb|CD955671.1|CD955671
EST:     CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGT                         GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
genomic: CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT

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), 45 (downstream exon)
Score: 55

CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 54

CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 37

CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT


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

CTACTTGCCTGAAGAGATGCGGAACCCAAATTCATTCAAGTgtacgtccac ... atttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccagagtttcttttccattttaaataatgattggtgctaatattatttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT
                                   tgctaat  putative branch site (score: 39)
                                           ttatttttct  CT-rich tract
                 attttaaataatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtccacaaatcctgatcagtgatcacatatttagataattaatacttcatatccagagtttcttttccattttaaataatgattggtgctaatattatttttctagGGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG