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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataacaaacgcaaagcacttgtgtatgtgggaagtacaattacgttctacattgttctatatcatttagcaattaactggacatacttgatcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA

Basic information

species Zea mays
transcript GRMZM2G102858_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 2
tataacaaacgcaaagcacttgtgtatgtgggaagtacaattacgttctacattgttctatatcatttagcaattaactggacatac-ttgatcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA
  ||    |  | |   |          ||   | |  |   ||   |||  ||   ||| ||| | | | | | | ||   ||| | ||  ||   ||||||| | || |  ||||||||||||||||||||||| || || ||||| ||||| ||||| || ||||| ||||| ||||| ||| ||||||||||| |||
-ttagtccattccatctagcaccactaatgaatactttatggacagactattttacactacatcgtgttgtattcagctaaccatgcattactcttttcagAGGCTAGCAGCTGGTGAGTGGTTTACAGCTCGAGTATCGTCTTGTGGACTTTTCCATATAGCATATCCAAGTGCTCCTGATCAATTGAAGGCAGAATTGA

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 2
------tataacaaac-gcaaagcacttgtgtatgtgggaagtacaattacgttctacattgttctatatcatttagcaattaactggacatacttgatcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA
      ||| |   |  | | ||  | ||  ||||| || |||  |  | |||| ||| | |||  | ||| |||    |||  ||      | ||| |    |||||| |||||   |||||| ||||| || |||||||| ||||||||||| || |||||||| || || ||||| |||||||||      |||  |||| |||
tcaatttatgatgcattgtatagatcctgc-tatgttggcagtttacattcgttttac-tggttgaacatcctttcaacattttct--tttaatttggtt---tcagAGATTGGCATCAGGTGAATGGTTCACTGCTCGAGTGTCTTCATGTGGACTATTTCATATTGCTTACCCTAGCGCACCTGAAATGTCAAAGATAGAATTGA

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 1
---tata-acaaacgcaaagcacttgtgtatgtgggaagtacaattacgttctacattgttctatatcatttagcaattaactggacatacttgatcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA
   |||  |   ||  | |  |  |||    |      ||  | |||   |   | ||   |   ||| |||  | || |  |    || ||||    | ||||||  ||||    ||||| |||||||| |||||||||||| ||||||| || |||||||| || || || ||||| || ||     | |||   ||  || 
gcatattcatttacctatataatgtgttaggggtttttgtgtagttaatattgtcgtttcgcctgatcttttgactatcatttat-tattcttg---tattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC

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|211520176|gb|FL353412.1|FL353412
EST:     CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAG                         AGGTTGGCGGTAGG
genomic: CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGG
EST: gi|60340984|gb|DN207957.1|DN207957
EST:     CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAG                         AGGTTGGCGGTAGGTGAGTGGTT-ACAG
genomic: CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAG
EST: gi|211350003|gb|FL351953.1|FL351953
EST:     CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAG                         AGGTTGGCGGTAGGTGAGTGGTTCACAGCTCGAGTTTCTTCATGTGGCCTT
genomic: CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTT
EST: gi|149079805|gb|EE168802.2|EE168802
EST:     CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAG                         AGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTT
genomic: CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTT
EST: gi|32866258|gb|CF005940.1|CF005940
EST:     GTGGACTGGTTTGCCCATGTCGTAAAG                         AGGTTGGCGGTAGGTGAGTGGTTCACCAGCTCGAGTTTCTTCATGTGGCCT
genomic: GTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTA-CAGCTCGAGTTTCTTCATGTGGCCT
EST: gi|148969766|gb|EE020648.2|EE020648
EST:     CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAG                         AGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTT
genomic: CACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTT

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), 49 (downstream exon)
Score: 209

GGAGACCTGCGTCAGAGACAAGGCTGTGGAATCACTTTGTCAGATAGGAGCACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 147

GGAGACCTGCGTCAGAGACAAGGCTGTGGAATCACTTTGTCAGATAGGAGCACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

GGAGACCTGCGTCAGAGACAAGGCTGTGGAATCACTTTGTCAGATAGGAGCACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 133

GGAGACCTGCGTCAGAGACAAGGCTGTGGAATCACTTTGTCAGATAGGAGCACAGATGAAGGAAAATGATATTGTGGACTGGTTTGCCCATGTCGTAAAGgtatgagcac ... atcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctacattgttctatatcatttagcaattaactggacatacttgatcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA
          ttctatatcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataacaaacgcaaagcacttgtgtatgtgggaagtacaattacgttctacattgttctatatcatttagcaattaactggacatacttgatcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- taacaaa
- - - - - - - - - - -gtgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggaca