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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGGACCTCTCTCCGTGGTTGAGTACAGCGAAATGGACGCAGCTATGACTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttctgtcctccacttgtcgttcccttccgccctacctccctccctccaaactgtaacagctgcatattttctcctctctctctctcgttttccccctcccctag

Basic information

species Zea mays
transcript GRMZM2G019986_T04
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019986_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 11
CGGTGGACCTCTCTCCGTGGTTGAGTACAGCGAAATGGACGCAGCTATGACTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttctgtcctccacttgtcgttcccttccgccctacctccctccctccaaactgtaacagctgcatattttctcctctctctctctcgttttccccctcccctag
 |||||||||||||| || |||||||| || |||||||||||||||||| ||||||| || |||||||| || || || || ||||| || |||||||| |||||  |||| ||||    || ||  ||||| | |      ||  |||  |      | ||||| | |||| || |   ||| ||                         
TGGTGGACCTCTCTCTGTAGTTGAGTATAGTGAAATGGACGCAGCTATGGCTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAATgtatg--ttctatcctttgtttctcaatccctcctggttgcactttctct-tgaggtgtataacaaccgcatgttcttatctcactgcag---------------------
















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|149111355|gb|EE294858.2|EE294858
EST:     CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|78089271|gb|DV517645.1|DV517645
EST:     AGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: AGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|211210620|gb|FL436849.1|FL436849
EST:     GGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: GGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|110497708|gb|EE015394.1|EE015394
EST:     ATCAATCAGTCGACAGGGGGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: ATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|16379775|gb|BI993142.1|BI993142
EST:     CGACAGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|71774723|gb|DR972601.1|DR972601
EST:     CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|148935255|gb|EC879292.2|EC879292
EST:     GAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: GAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|18166601|gb|BM336440.1|BM336440
EST:     AGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: AGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|40335845|gb|CK369915.1|CK369915
EST:     CTACTGAGATCAATCAGTCGACAGGACGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|149102321|gb|EE287688.2|EE287688
EST:     ATCAATCAGTCGACAGGGGGACTCCGTTACTGCGGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: ATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|67018099|gb|CO446848.1|CO446848
EST:     CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|37375243|gb|CF624047.1|CF624047
EST:     CTACTGAGATCAATCAGTCGACAGGACGACTCCGTTACTGCTGGAGCAAC                         ATCTGCNTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|17931736|gb|BM268696.1|BM268696
EST:     CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
EST: gi|40303710|gb|CK348097.1|CK348097
EST:     CGACTCCGTTACTGCTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC
genomic: CGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGC

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: 48 (upstream exon), 40 (downstream exon)
Score: 137

CGGTGGACCTCTCTCCGTGGTTGAGTACAGCGAAATGGACGCAGCTATGACTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 114

CGGTGGACCTCTCTCCGTGGTTGAGTACAGCGAAATGGACGCAGCTATGACTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 98

CGGTGGACCTCTCTCCGTGGTTGAGTACAGCGAAATGGACGCAGCTATGACTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 728

CGGTGGACCTCTCTCCGTGGTTGAGTACAGCGAAATGGACGCAGCTATGACTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttc ... cctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTGGACCTCTCTCCGTGGTTGAGTACAGCGAAATGGACGCAGCTATGACTACTGAGATCAATCAGTCGACAGGGCGACTCCGTTACTGCTGGAGCAACgtatggtttctgtcctccacttgtcgttcccttccgccctacctccctccctccaaactgtaacagctgcatattttctcctctctctctctcgttttccccctcccctag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA