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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagtcttgcacttgtttcataccctgacatcgtcaagtattctactattctacagtatgctaatgctggtgttgttgttgggtgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG

Basic information

species Zea mays
transcript GRMZM2G069816_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069816_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 5
gtgagc---agtcttgcac---ttgtttcataccctgacatcgtcaagtattctactattctacagtatgctaatgctggtgttgt-tgttgggtgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG
|| ||     || ||| |    ||||||||     |||   |   || |||||  ||  || |||  |   || | ||  |  ||| |  ||  || ||| |||||||| ||||||||||||||||||||  ||||||| |||||||||||||||||||||| |
gtaagttcttgtattgtatgcgttgtttcaccttttgatgccag-aattattcctcttctccacataaccttagtactcatactgtgttgtgtctggcccatagACGGAGGATGAGAAGGAAATGGTCATAAGAACTGTTTATTGTACAAACATAGATAAGAAG
















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|211272638|gb|FL458520.1|FL458520
EST:     TCCAAAGTTTCTTCCCAGG                         ACGGMCGATGAGAAGGAAATGGYCATGCGAACTGTCTATTGTACAWATATA
genomic: TCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|78092729|gb|DV521103.1|DV521103
EST:     TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGG                         ACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|37385479|gb|CF629884.1|CF629884
EST:     TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGG                         ACGGACGATGAGAAGGTAATGGTCATGCGTACTGTCTATTGT
genomic: TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGT
EST: gi|60352077|gb|DN219050.1|DN219050
EST:     TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGG                         ACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|149097331|gb|EE183163.2|EE183163
EST:     TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGG                         ACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|211064466|gb|FK995272.1|FK995272
EST:     CTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAATATA
genomic: CTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|78092728|gb|DV521102.1|DV521102
EST:     TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGG                         ACGGAGGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|149096648|gb|EE182414.2|EE182414
EST:     GCCTTCAAAGACAGCTATCTTACCCCGT-AATCCCAAGTTTCCTCCCAGG                         ACGGACGATGAGAAG
genomic: GCCTTCAAAGACAGCTATCTTACCC-GTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 130

TGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 185

TGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

TGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

TGCACTTAACCTCGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCTTCAAAGACAGCTATCTTACCCGTTAATCCAAAGTTTCTTCCCAGGgtgagcagtc ... tgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctactattctacagtatgctaatgctggtgttgttgttgggtgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG
                    tgctaat  putative branch site (score: 158)
     tactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagtcttgcacttgtttcataccctgacatcgtcaagtattctactattctacagtatgctaatgctggtgttgttgttgggtgtcccgtagACGGACGATGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG