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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttctgacagttttacatactggattaagaactaacctgcttcatgaccttcgtaccttaccatcattgtgctttgcag

Basic information

species Zea mays
transcript GRMZM5G864414_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864414_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g02550.1 (Oryza sativa), 5'ss of exon 14
TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttctg---acagttttacatactggattaagaactaacctgc---ttcatgaccttcgtac-cttaccatcattgtgctttgcag----------------
||||| |||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||| ||  |||||   |    ||| |||| |  || | ||||| |  |     ||   |    | |||   ||   ||  |      |   |                 
TGGCTCTGCTCATGGGACCCACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttctggttattactttccatagtacatgatgaacttatttatgagtttgcggtagttgtatatttgttattttgaaatatcataattgtttttttttacag
















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|32837059|gb|CD976737.1|CD976737
EST:     CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
genomic: CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
EST: gi|20301126|gb|BQ164069.1|BQ164069
EST:     CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
genomic: CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
EST: gi|111433841|gb|EE298127.1|EE298127
EST:     ACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTAGNNTTCGG                         CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGC
genomic: ACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCT-TCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGC
EST: gi|71448844|gb|DR829894.1|DR829894
EST:     GGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
genomic: GGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
EST: gi|60395565|gb|DN228435.1|DN228435
EST:     CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
genomic: CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
EST: gi|32838225|gb|CD977903.1|CD977903
EST:     CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTATGTCCCACCTTCACTTCGCAAAAAATCTACTGGATATGCA
genomic: CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
EST: gi|18963937|gb|BM660714.1|BM660714
EST:     CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
genomic: CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
EST: gi|71417221|gb|DR803973.1|DR803973
EST:     CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA
genomic: CACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCA

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: 156

TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 407

TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 396

TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 255

TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttc ... tgctttgcagCCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttctgacagttttacatactggattaagaactaacctgcttcatgaccttcgtaccttaccatcattgtgctttgcag

- - - - - - - - - -  CGAAGA
- - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - TGGAGG