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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTTCTGAAACACATTGATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctcacttgcttaaaagggaaacaatgtactataaagtagctcctttatttttttctcgaatacgttggagagctacgtatcattatattaatag...

Basic information

species Zea mays
transcript GRMZM2G044011_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 5'ss of exon 9
GCATTTCTGAAACACATTGATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctcacttgcttaaaagggaaacaatgtactataaagtagctcctttatttttttctcgaatacgttggagagctacgt-atcattatattaatag-----
|| || ||||| || |||||||||||||| ||||| ||| ||||||||||||||||||||||||| |||||||||||||| | |||| |           ||  |||||  | | |   | ||   | | || |  || |       | |  | || | | || |  | |     
GCTTTCCTGAAGCATATTGATTTTGAAGTAGTCCAATGTGCTGTAATTGCAAGCCCAGGTTTTACTAAGgtaatcctcacgtacttacagttttg-----gttttataagttggtttggt-atccatgtgtcaagcacatgatgatacaattttatgaatttagtttttgtttat
















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|67018605|gb|CO447354.1|CO447354
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGTGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGTGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|71763506|gb|DR961443.1|DR961443
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|74236267|gb|DT644181.1|DT644181
EST:     CCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: CCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|71442136|gb|DR823186.1|DR823186
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|50333168|gb|CO528294.1|CO528294
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|32825337|gb|CD965059.1|CD965059
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATT
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATT
EST: gi|71302744|gb|DR787484.1|DR787484
EST:     TTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: TTTGAAGTTGTCCAGTGTACTGTAATTGCAAG-CCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|76016282|gb|DT943452.1|DT943452
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA

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: 47 (upstream exon), 47 (downstream exon)
Score: 105

GCATTTCTGAAACACATTGATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GCATTTCTGAAACACATTGATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

GCATTTCTGAAACACATTGATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 134

GCATTTCTGAAACACATTGATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTTCTGAAACACATTGATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctcacttgcttaaaagggaaacaatgtactataaagtagctcctttatttttttctcgaatacgttggagagctacgtatcattatattaatag

- - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaacaa