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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttttttgtttgtaccgaacaatgaaaattcttcagaattatcatgttctcaaagcaaattgtcaaatcacaacatgtgtacacagtcacacacgcatgcatgttaaaggtcctatttggtaagctgataacaatggtccactgcatctactgtcaacttttatggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG

Basic information

species Zea mays
transcript GRMZM2G152127_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 5
gtaagcttttttgtttgtaccgaacaatgaaaattcttcagaattatcatgttctcaaagcaaattgtcaaatcacaac-atgtgtacacagtcacacacgcatgcatgttaaaggtcc-tatttggtaagctgataacaatggtccactgcatctactgtcaacttttatggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG
|||||  ||  || ||  |  ||  |     ||  | | | |||| |     |||  ||     || |   |   |||  ||  |||      |||| |  | ||||| | || |||   |  ||| |       |||||||| |||    |||||    |||  || | ||| ||||||||| ||||| ||||||||  || |||||||||| |||||| ||||||||||| | |||||||||||||| ||||||
gtaag--ttgctggtttcattgagaaccaggaacacatga-aattgta----tctggaactttttttttggaaagcaattatcagtatcacaacacataaacgtgcatttgaatggtagatgcttgtt-------taacaatgctccctgacatcttgcatcattttctgtggttgtagGTGCTGGGGCTGTAGAATTTATACTGTGCCATGCTGAGGTAGAAATTGCTTTTATAGAGGAAAAGAAGATAGGAGAG
















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|32868449|gb|CF008131.1|CF008131
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAGATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|91055766|gb|EB166184.1|EB166184
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|76919428|gb|DV167710.1|DV167710
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGC
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGC
EST: gi|76014959|gb|DT942129.1|DT942129
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|32867927|gb|CF007609.1|CF007609
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAGATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|74239653|gb|DT647567.1|DT647567
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|71426983|gb|DR808033.1|DR808033
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|148958182|gb|EC904386.2|EC904386
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGAGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|148961536|gb|EE012289.2|EE012289
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
EST: gi|24766862|gb|CA402007.1|CA402007
EST:     GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTG                         GTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT
genomic: GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTT

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: 112

GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 61

GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 31

GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 173

GCCTGCAATGCCCATGGCATCTACTGTGTGCCACTATATGACACGCTTGgtaagctttt ... atggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtaagctgataacaatggtccactgcatctactgtcaacttttatggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG
        tgataac  putative branch site (score: 173)
                                        cttttat  putative PPT
                                      aacttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttttttgtttgtaccgaacaatgaaaattcttcagaattatcatgttctcaaagcaaattgtcaaatcacaacatgtgtacacagtcacacacgcatgcatgttaaaggtcctatttggtaagctgataacaatggtccactgcatctactgtcaacttttatggctgtagGTGCCGGGGCAGTAGAATTCGTATTGTGCCATGCAGAGGTACAAATTGCTTTTGTTGAGGAAAAGAAGATCGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG