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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttccaagtgaacagttactttatcttgtgtatttgtttgtgggggttagtttttgagtcaggcttaatgtgtaaaagccaattcaacgattcat...

Basic information

species Zea mays
transcript GRMZM2G028096_T04
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028096_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 2
AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttccaagtgaacagttactttatcttgtgtatttgtttgtgggggttagtt--tttgagtcaggcttaatgtgtaaaagccaattcaacgat-tcat
|||||||||||||| || ||||||||| ||||||||||||| |||||||| ||||||||||  |  |   |    | ||  || |||    |   |    ||| |||||   ||| ||| ||  ||  ||||| ||    |||  |    |  |||
AAGATGGACATGGGGCCATGCCCGAAGATGCACTCGCTGCAGCTGCGCAAGGAgtatccttggagatccccttcaaattattcatgtagggtaact---agggtttagtatgtttcagttagattttgtgtgtgaatagaaatagatttgtgccat
















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|211342903|gb|FL126052.1|FL126052
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTATTGATAACTATGACCGT
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGT
EST: gi|211342904|gb|FL126053.1|FL126053
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGKGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342898|gb|FL126047.1|FL126047
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGC-AAAGCCAAAGGTACTGATAACTATGGACCGTGGAATTG
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATG-ACCGTG-AATTG
EST: gi|211342902|gb|FL126051.1|FL126051
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211340511|gb|FL126040.1|FL126040
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342905|gb|FL126054.1|FL126054
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342900|gb|FL126049.1|FL126049
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|71764556|gb|DR962493.1|DR962493
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|74232160|gb|DT640074.1|DT640074
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342892|gb|FL126041.1|FL126041
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGC-AAAGCCAAAGGTACTGATAACTATGGACCGGGGAATTG
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATG-ACCGTG-AATTG
EST: gi|211342897|gb|FL126046.1|FL126046
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342893|gb|FL126042.1|FL126042
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342896|gb|FL126045.1|FL126045
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211340507|gb|FL126036.1|FL126036
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTATTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211340510|gb|FL126039.1|FL126039
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTG
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTG

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), 48 (downstream exon)
Score: 247

AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 98

AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 102

AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 96

AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttccaagtgaacagttactttatcttgtgtatttgtttgtgggggttagtttttgagtcaggcttaatgtgtaaaagccaattcaacgattcat

- - - - - - - - - - - - AAGCTG
- - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - GCAAAG