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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaag

Basic information

species Zea mays
transcript GRMZM2G158162_T03
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 4
GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttag--taacttatacatca---aggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttctttta-tcttccttgactatattt---tgcaag
||||||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||| || ||||| ||||||||||||||||                  ||  |  | | |||||| |||||| |||   |  |   |  ||   ||  ||    || |   |  ||||  ||  | ||| |  |    ||   || | ||||  ||||||  | | |       | ||| | | |  | ||||  | |||||| |||||||||   | ||||
GTGTTGCAAGGCCACCTGCAGAAGGTAGGGGCCGCAATCAATTACTTCCTCGATATTGGCCTAGAATAACAGACCAAGAGCTACAGCAAATTTCTGGAGAgtatcctta-----------------ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatt-tcatattgtgcatacctattt-------ctgatctggatgctattttggttttccttaactatatttctcttcaag

upper sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G32810.1 (Glycine max), 5'ss of exon 9
GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataat-atgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaag
            |||||||||||||| ||||  | |||||||| ||||| || |||||||| || || || || |||||| ||||||||||||| |||||||||||   ||             ||     | | ||||   |    |||||     || |    || |   ||||||  || |    |  | |     || |||   |   |      |||  ||||| ||| |  |  |   |                                               
------------CACCTGCTGAAGGACGGGGAAGGAATCAATTGCTTCCACGTTATTGGCCTAGGATTACTGATCAAGAGTTGCAACAAATATCAGGAGAGTATCCAACATTgtaatctgtcctataaattattatgaatcac----tgacaggatacttactggttgatacacttat-tatta--ttttgatagctaatctttaccttagtatttccttaaccatgattcatgatatgttcaag-----------------------------------------------

upper sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G04330.1 (Glycine max), 5'ss of exon 6
GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaag
            |||||||||||||| ||||  | |||||||| ||||| || |||||||| || || || || |||||| ||||||||||||| |||||||||||    |      |   |  ||     | | | || |  ||||    ||   |  || |  || |  |||||||  || |    |  | |    ||| |||  | | |    ||     |  || ||| |  |  |   |                                               
------------CACCTGCTGAAGGACGGGGAAGGAATCAATTGCTTCCACGTTATTGGCCTAGGATTACCGATCAAGAGTTGCAACAAATATCAGGAGAGTATCCAGCGTTgtaattagttctataaattattattaa-tcactggcaggat-acttacacaggttaataaacttat-tattat--tttgatagctactcttta--ccttagtatttccttaaccattcatgatatgttcaag-----------------------------------------------

upper sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0058g01300.t01 (Vitis vinifera), 5'ss of exon 5
GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttgataaggtctccatacatttgaaact-gtgaacttcctgg-tgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaag
||||||| ||||||||||| || ||| |||| || ||||| || |||||||| |||||||| || || |||||||| ||  |||| ||||||||||||||||||||||||  | |||    |   ||||||  |  |  | | | | | ||  | |  | |   |  |||  |  ||||| || |||  |  |     |  || |||  | |     |||  |                                                                      
GTGTTGCAAGGCCACCTGCAGAGGGACGGGGTCGGAATCAGTTGCTTCCTCGTTATTGGCCGAGGATCACAGACCAGGAATTGCAGCAAATATCTGGAGAgtatccttgactatgtcatttttattttgaagttcatagattgcttcgctgttaatttttttttaattttcatg-cttattcaccaactcgatcagcgatttctttaatcatgctttcttgaag---------------------------------------------------------------------

upper sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0004g08100.t01 (Vitis vinifera), 5'ss of exon 4
GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaag
|  |||| |||||||||||||| || ||||| || ||||| ||||||||||| || |||||||| || || ||||| || ||||| ||| ||||||||||||||||   ||||    | ||||| ||   || | | || ||  |  | |   | ||   |     ||  | |  || ||||  |   | | |  | | ||||| |  | ||     | |  ||   | ||||  ||   |                                                  
GCATTGCAAGGCCACCTGCTGAGGGGAGGGGACGGAATCAGTTACTTCCTCGATACTGGCCAAGGATTACCGACCAGGAACTGCAGCAATTATCTGGAGAgtatcc---ataaatatttcatacttt---aatttttaagttgattatcatcataatagaatgtgatt--ttatgta-acattcaatgtgttggtttgttcatt-gattcaattaagtgtt-taccttacatatgttatcttcaag---------------------------------------------

upper sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 4
lower sequence: PP1S31_242V6.1 (Physcomitrella patens), 5'ss of exon 5
GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATA---TCTGGAGAgtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttataca-tcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaag
   | ||  |||||||||  || |||||||| ||||| || || || ||||| ||||||||  ||||||||||||| |||||| | || ||    ||||||||||||||||  ||||   |   |  |||  ||  |||| |  |   ||| ||     ||   ||  ||     |    |||| || |  ||  ||  |   ||| | | |  ||  | ||| |                                                                      
---TAGCGCGGCCACCTGGAGAGGGAAGGGGTCGCAACCAGTTGCTACCTCGTTATTGGCCTCGAATAACAGACCAGGAGCTGAAGCAGATCAATTCTGGAGAgtatcctttctaag---tttgtttattcaaatttgtgtaaataggggttacgggattcagtgagtttcgagtatcattacaatctaatcttcagttt---tcacttgac--aatgcattacag---------------------------------------------------------------------

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|5268958|gb|AI770922.1|AI770922
EST:     CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGAGA
genomic: CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA
EST: gi|67040653|gb|CO466908.1|CO466908
EST:     CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA
genomic: CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA
EST: gi|13150757|gb|BG321079.1|BG321079
EST:     AACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTSA
genomic: AACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA

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), 46 (downstream exon)
Score: 106

GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 215

GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA