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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactctctctctctctcaacatgtgtatacacttccccgccctgacagacacccatcaaccaacccctcaattatctgactaccttatttcctttgcag

Basic information

species Zea mays
transcript GRMZM2G014116_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 7
TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactctctctctctctcaacatgtgtatacacttccccgccctgacagacacccatcaaccaacccctcaattatctgactaccttatttcctttgcag
 |||||||| ||||||||||||||| |||||||||||||||| |||||| | |||||||| |||||| ||||||||||||||||| ||||||||||||||||| |    |||||||  || |||    |   |    |     |  |  | |  ||| ||      ||        |||||||||| ||| | |||  ||  ||
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaag---ctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataat-----ggttatctgactgcctgaattcgctt-tag
















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|211388540|gb|FL326080.1|FL326080
EST:     CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCG                         ATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
genomic: CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
EST: gi|7216589|gb|AW562711.1|AW562711
EST:     CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCG                         ATTCTTAGGAAGATCTGTTGGTACTTGGNGCTAGCACCTCATGATCCTATG
genomic: CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
EST: gi|211150172|gb|FL276377.1|FL276377
EST:     CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCG                         ATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
genomic: CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
EST: gi|213188018|gb|FM188229.1|FM188229
EST:     CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCG                         ATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
genomic: CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
EST: gi|26457612|gb|CA829195.1|CA829195
EST:     CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCG                         ATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
genomic: CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
EST: gi|213183945|gb|FM195837.1|FM195837
EST:     CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCG                         ATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG
genomic: CTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATG

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: 425

TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 397

TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307

TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactc ... tcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactctctctctctctcaacatgtgtatacacttccccgccctgacagacacccatcaaccaacccctcaattatctgactaccttatttcctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA