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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaatttactttgttgtgtttctgttagtgctgacatgtacattgtatttttcgatatgatttggaatattgcttctggccaccttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT

Basic information

species Zea mays
transcript GRMZM2G149994_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149994_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g42110.1 (Oryza sativa), 3'ss of exon 3
gtactgaatttactttgttgtgtttctgttag-------tgctgacatgtacattgtatttttcgatatg--atttggaatattgcttctggccaccttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT
||| ||| || |||    |  |||    ||         ||||    | |  |||| || ||| ||| ||  | ||     |     | |    |  || ||||  ||  |||||| || ||| |||| |  |||||||| || |||||| |||| || |||||| ||||||||||||| ||||| |  | ||||| |||||| 
gtaatgacttaactcgaattggttaaccttgaaagactctgctttgcttttaattgcatattttgatttggcacttaattcacataatgtacatatgtttacagTTCAATTTCTGTGCATAAACCCCACGCTGGAGAGGGGGAGAAGTTCATGCGAGAGGCTTTTACTGAAGCATATTCCCAGGCATCACAGGGTAGACCAGCC
















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|211510550|gb|FL129059.1|FL129059
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAATGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
EST: gi|211510555|gb|FL129064.1|FL129064
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAATGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
EST: gi|211510558|gb|FL129067.1|FL129067
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAATGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
EST: gi|211510556|gb|FL129065.1|FL129065
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAATGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
EST: gi|211512912|gb|FL129068.1|FL129068
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAATGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
EST: gi|71445517|gb|DR826567.1|DR826567
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
EST: gi|211512914|gb|FL129070.1|FL129070
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAATGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
EST: gi|211510557|gb|FL129066.1|FL129066
EST:     CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAATGATCAA                         CCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG
genomic: CTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCG

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: 135

ACAAGCCTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 89

ACAAGCCTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

ACAAGCCTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

ACAAGCCTGGTTCGAGCTATTGTTCGAGAATGCAACGCGCACCTGACAACGATCAAgtactgaatt ... accttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacattgtatttttcgatatgatttggaatattgcttctggccaccttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT
                                           ccacctt  CT-rich tract
     attgtattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgaatttactttgttgtgtttctgttagtgctgacatgtacattgtatttttcgatatgatttggaatattgcttctggccaccttgacagCCCATATTCTGTACACAAAGCCCATGTGGGAGAGGGAGAAAAGTTCCTGCGTGAAGCTTTTTCTGAAGCATATTCTCAGGCTTTGCGGGGTAAACCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC