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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctgaacgtgggcttgcatgcaggggggtggggggaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcacgcttgtctactatgtgcag

Basic information

species Zea mays
transcript GRMZM2G017941_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017941_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g03380.1 (Oryza sativa), 5'ss of exon 8
---GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctgaacgtgggcttgcatgcaggggggtggggggaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcacgcttgtctactatgtgcag
   | |||| || |||| ||| ||   ||| ||| ||||||      | ||||||||||| |||||| |||| ||||||||||| || ||||||| |||||| |||||| || |    |    || | |  ||| |      |  |  | | ||||||  |||     |       |      ||| |  |  |  |||   |||                                                 
CAGGTACCTCGCAGAGAAGACCAATACTACTAAACCTGGCCGT---GGAAAATGTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtctcatggactcctatgtttttgtttacctttctttctgtcaacgtgaacttaagcccgtacatatcaaacaaaaacggtaatcagtt--tagt-------------------------------------------------

upper sequence: GRMZM2G017941_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g03060.2 (Oryza sativa), 5'ss of exon 8
------GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctga-acgtgggctt--gcatgcaggggggtggggggaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcacgcttgtctactatgtgcag
      | |||| || |||| ||||||   ||| ||| | ||||      | |||||||| || |||||| |||| ||||||||||| || ||||||| |||||| |||||| ||   | ||  || | |||  ||  | |||  ||  ||||||  | || | |||  || |  |  |   |      ||| |  | | |  ||                                                       
AGGCAGGTACCTCGCAGAGAAGACTAATACTACTAAACCCGGCCGT---GGAAAATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagttgtcc-catggactgtttttt-ttattggttactttcattctgtcatgtagacttaagcctataatgttttccaacaaaaacagtataatttt-------------------------------------------------------

upper sequence: GRMZM2G017941_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 8
---GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctga-acgtgggctt--gcatgcaggggggtggggggaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcacgcttgtctactatgtgcag
   | |||| || |||| ||||||   ||| ||| | ||||      | |||||||| || |||||| |||| ||||||||||| || ||||||| |||||| |||||| ||   | ||  || | |||  ||  | |||  ||  ||||||  | || | |||  || |  |  |   |      ||| |  | | |  ||                                                       
CAGGTACCTCGCAGAGAAGACTAATACTACTAAACCCGGCCGT---GGAAAATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTTgtaagttgtcc-catggactgtttttt-ttattggttactttcattctgtcatgtagacttaagcctataatgttttccaacaaaaacagtataattttaga----------------------------------------------------

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|78025308|gb|DV493695.1|DV493695
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|211169629|gb|FL169502.1|FL169502
EST:     TTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAAGAACCTTTGTC                         GGGAATAGTGCTCCCTTATCAATCT-GATATCAGGGCCTCATGGTGTATGA
genomic: T-GACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGG-AATAGTGCTCC-TTATCA-TCTTGATATCAGGGC-TCATG-TGTATGA
EST: gi|60401365|gb|DN234172.1|DN234172
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|16925942|gb|BM079010.1|BM079010
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|110524419|gb|EE028603.1|EE028603
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|37373929|gb|CF623288.1|CF623288
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|16379938|gb|BI993223.1|BI993223
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|37383723|gb|CF628888.1|CF628888
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|71329487|gb|DR801465.1|DR801465
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|37379701|gb|CF626599.1|CF626599
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|4834965|gb|AI670191.1|AI670191
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|211093959|gb|FL454783.1|FL454783
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|18180439|gb|BM381649.1|BM381649
EST:     AGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: AGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|211106366|gb|FL481491.1|FL481491
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|16917407|gb|BM073272.1|BM073272
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|149013783|gb|EE043247.2|EE043247
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|67024634|gb|CO453383.1|CO453383
EST:     GACGGAGAGTGCCTAGTNCAAATCA-CTCTTTCT-GAANGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GACGGAGAGTGCCTAGT-CAAATCAACTCTT-CTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|78106617|gb|DV525035.1|DV525035
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|4730421|gb|AI649587.1|AI649587
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|37397410|gb|CF636002.1|CF636002
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|32844930|gb|CD984611.1|CD984611
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|113702062|gb|EE679566.1|EE679566
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
EST: gi|37387018|gb|CF630701.1|CF630701
EST:     GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTC                         GGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA
genomic: GTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGA

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: 137

GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGAATCGATACTCCCTCCAAGTTTGAAGCTCCCCAGGAGTCTTGATCTCCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 344

GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGAATCGATACTCCCTCCAAGTTTGAAGCTCCCCAGGAGTCTTGATCTCCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGAATCGATACTCCCTCCAAGTTTGAAGCTCCCCAGGAGTCTTGATCTCCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtt ... ctatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGAATCGATACTCCCTCCAAGTTTGAAGCTCCCCAGGAGTCTTGATCTCCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctgaacgtgggcttgcatgcaggggggtggggggaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcacgcttgtctactatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA