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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagactaaaagttgtttttatgtatgatagtttgcagtagtacttatacatatactgctcttttccaaaatgctgactgatttacactctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC

Basic information

species Zea mays
transcript GRMZM2G057408_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057408_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 7
ttgagactaaaagttgtttttatgtatgatagtttgcagtagtacttatacatatactgctcttttccaaaatgctgactgatttacact--ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC-
 ||  | |||  |    ||||||||   | |     || | | | ||          || | |  | |||  | |||||   || || ||  ||||||||||| ||| ||||| ||||||| ||  | ||||||   |||||   | || ||||||| ||||||||||||||||||||| |||||| ||||||| || | |  
atgtcaataagggcatattttatgttctaca--caacacttgcatttgacttcgatttgttatagtgcaatgtcctgacattttgactctacctgattgcagCTGAGCTTGCTGTCATCATGTAATTCTGGTGG---GGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT
















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|71428976|gb|DR810026.1|DR810026
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|78118281|gb|DV536668.1|DV536668
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|148939135|gb|EC883572.2|EC883572
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|60336979|gb|DN203952.1|DN203952
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|91876491|gb|EB406448.1|EB406448
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGGCCATGTCAAATCT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|60397572|gb|DN230388.1|DN230388
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|110220916|gb|EC902814.1|EC902814
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|50322593|gb|CO517719.1|CO517719
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATTT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT
EST: gi|71763063|gb|DR961000.1|DR961000
EST:     TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT                         CGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGGCCATGTCAAATTT
genomic: TTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCT

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), 42 (downstream exon)
Score: 29

GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 16

GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 29

GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 22

GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACATgtaagttatt ... ctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatacatatactgctcttttccaaaatgctgactgatttacactctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC
      atatact  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagactaaaagttgtttttatgtatgatagtttgcagtagtacttatacatatactgctcttttccaaaatgctgactgatttacactctgattgcagCGGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC