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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtctatttttgttttacatgtgatacttggatttgttattttaaccttggttgcatctagagggtactatcatataagggcagaagactaatgaaaaatgacccaactgtattttttgtgcattgagtaacccaaacttatcgctccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT

Basic information

species Zea mays
transcript GRMZM2G461145_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g51540.1 (Oryza sativa), 3'ss of exon 4
gcaagtctatttttgttttacatgtgatacttggatttgttattttaaccttggttgcatctagagggtactatcatataagggcagaagactaatgaaaaatgaccc--aactgta--------------ttttttgtgcattgagtaacccaaacttatcgctccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT
|||||| ||||  | |||| | || ||||| | |   | || ||| ||| ||   |  |||||||   || | |  |  ||  |  ||||  ||||||||||    ||  ||||| |              |    | || || |||||    |||||||| ||| ||||  ||||||||||||||||||| ||||||||| || | |||||| |||| ||||||||||||||||||||||||||||||||| | |||||| |||||||||| ||
gcaagtttattcatatttt-cttgggataccttgtaatatt-tttcaacttt---tatatctagaacatattgt--ttaaaaagtggaagcgtaatgaaaaaacgtcctaaactgcaaaagtaaacaccaataaactctgaatagagtattttaaacttattgcttcttatgcagGACACTATGAGAGGCCCCCATACAATGAAAACACTATAAGGTCAGTGTACCATGTAAGGCATTATGATGTTCTCAAGTTAATGCATGTGAAGGAGCCTCT
















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|67037524|gb|CO464338.1|CO464338
EST:     ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAG                         GACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
genomic: ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
EST: gi|5847378|gb|AW000457.1|AW000457
EST:     ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAG                         GACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
genomic: ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
EST: gi|4730521|gb|AI649687.1|AI649687
EST:     ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAG                         GACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
genomic: ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
EST: gi|31357484|gb|CD441841.1|CD441841
EST:     ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAG                         GACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
genomic: ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
EST: gi|32832676|gb|CD972354.1|CD972354
EST:     ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAG                         GACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
genomic: ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
EST: gi|32833679|gb|CD973357.1|CD973357
EST:     CGAATTGGTGGATTGTCTGGTANT-CTTAACAAACACCATTATCATTTAG                         GACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
genomic: CGAATTGGTGGATTGTCAGG-AATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
EST: gi|32836175|gb|CD975853.1|CD975853
EST:     ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAG                         GACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC
genomic: ACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACC

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: 45 (upstream exon), 49 (downstream exon)
Score: 45

CCTAACATATACTTTTTGGGGTTTGCTGGTGTTGTTAAGTTTGGAAACATACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 33

CCTAACATATACTTTTTGGGGTTTGCTGGTGTTGTTAAGTTTGGAAACATACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 22

CCTAACATATACTTTTTGGGGTTTGCTGGTGTTGTTAAGTTTGGAAACATACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 19

CCTAACATATACTTTTTGGGGTTTGCTGGTGTTGTTAAGTTTGGAAACATACGAATTGGTGGATTGTCAGGAATACATAACAAACACCATTATCATTTAGgcaagtctat ... ccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccaactgtattttttgtgcattgagtaacccaaacttatcgctccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT
                                            tccttac  putative branch site (score: 19)
                                        tcgctcctt  CT-rich tract
       tgtatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtctatttttgttttacatgtgatacttggatttgttattttaaccttggttgcatctagagggtactatcatataagggcagaagactaatgaaaaatgacccaactgtattttttgtgcattgagtaacccaaacttatcgctccttacacagGACACTATGAGAGGCCTCCATACAATAAAGATACTATACGGTCTGTGTACCATGTAAGGCATTATGATGTTCTCAAGCTCATGCATTTGAAGGAGCCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG