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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttggatcacttatttagttatagtcttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA

Basic information

species Zea mays
transcript GRMZM2G132804_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
-------------gttcttggatcactta--tttagttatagtcttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
              ||||    ||| ||   |||  ||| |   |  |  |   | | | |   ||| ||  |    ||  ||||| |||  ||||| |||||||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||||
gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcattactctaattattttgctcg--taacttcttcctg-tagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
---------------------------------------------gttcttggatcacttatttagttatagtcttcgatg-cagtaagt-ttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                                              |  || ||    || | ||  | ||    | | |  |  | ||  |||  |   ||||| | || | |     ||| |||||||||||||| || || |||||||| ||||||||||||||| | |||||||| |||||||| || || |||||||| || ||||| || ||||| ||||
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
------------------------------------gttcttggatcactt---atttagttatagtcttcgatg-cagtaagt-ttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                                     ||    | | | ||   || |   | ||    | | |  |  | ||  |||  ||  ||||| | || |  |   ||   |||||||||||||| || ||||||||||| ||||||||||||||| | ||||| || |||||||| || || ||||| || || ||||| || ||||||||||
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttg--ttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gttcttggatcacttatttagt----tatagtcttcgatgca-gtaagtttgtctatattattaaatta--gattctt----actgg-cagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                         | |   | ||  ||  | |  |    | |   |||  ||  | ||||     | |||  |  |||  ||  |||| ||    ||||  ||||| ||||| || || || |||||||| | ||| ||||||||| | ||||||||||||||||| || || ||||||||||| ||||| ||||| || ||||
gtatttttttagccctgtttggtcagatgacgcattcctgctctgttctcatgtgcccttatatatatgtaaaacattttattatggtaatctaaggatttttggacactgaacagATTTTGAAAGAACTTCACAAATCTTGTCGAAGAGAAGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------gttcttggatcacttatttagttatagtcttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                        | | | || |||| | |||||  | |      | |||||   |  | | |  |  | |   |   || |      |||| ||||||||||| || |||||||| |||| |||||||||  | ||||| || ||||| ||||| |||||  ||||||| ||||| |||||||| || |
actccttggtatacatcagtgttatgtagaataacttttatagttgcactgcatcgt-cagtagcatcatatgtgatgctgaccaatggtcgtgtgtttagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------gttcttggatcacttatttagt-tatagtc--ttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                                                                                              | ||  |      || || | | ||||   |||  ||   | ||      | |  || | |       || |||  |||||| ||||||||||| ||||||||||| || | |||||||||| | ||||| || ||||| ||||||||  |  |||| || ||||| || || || || |
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacagcttgtcgtacgtgcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------gttcttggatcacttatttagttatagtcttcgatgcagtaagtttgtctatat-----tattaaat-----tagattcttactg--gcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                                                                              |           | | || |  |||    |      | ||  ||| |   ||      | | | ||     ||  ||||||     |||||| ||||||||||| || |||||||| || |  ||||||||| | |||||||| ||||| ||||||||  |  | || || ||||| || || || || |
gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgttcgcagaatatattttttcgtacacaaatgtgagatgcttctaatttcttagaactgcagATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 5
gttcttggatcacttatttagttatagtcttcgatgcagtaagtttgtctatattattaaattagattcttactg-gcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                        || | || |     || | ||| | || ||| |          | |  |||   |||| ||||| ||||| || | ||| ||||| || |||||||| ||||||||||| |||||||| || |||||| ||||||| || || ||||| || || |
-----------------------gtaatattagcctgggtgatttttttta-attttctggccctcctttcgctgcatagATTTTGAAAGAGCTCCACAGATCGTGCCAGAGAGAAGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGA

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 5
gttcttggatcacttatttagttatagtcttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                        || |||| |     || | |||    || || | |   |  |||||       |||| ||||| ||||| || | ||| ||||| || |||||||| ||||||||||| |||||||| || |||||| ||||||| || || ||||| || || |
-----------------------gtaatcttagcctgggtgatttttctaattttctgacccttcattctctgca-tagATTTTGAAAGAGCTCCACAGATCGTGCCAGAGAGAAGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGA

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|32933387|gb|CF038199.1|CF038199
EST:     AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAG                         ATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
genomic: AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
EST: gi|9731371|gb|BE510123.1|BE510123
EST:     AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAG                         ATATTGAAGGAGTTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
genomic: AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
EST: gi|9461676|gb|BE453849.1|BE453849
EST:     AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAG                         ATATTGAAGGAGTTGCATAAATCTTGCC
genomic: AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCC
EST: gi|33094377|gb|CF054371.1|CF054371
EST:     AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAG                         ATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT
genomic: AGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGAT

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), 48 (downstream exon)
Score: 144

AGATTATGGTTCAAGACAAACTTGAAGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

AGATTATGGTTCAAGACAAACTTGAAGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

AGATTATGGTTCAAGACAAACTTGAAGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 70

AGATTATGGTTCAAGACAAACTTGAAGCTCTGCAAAATTTGGTTTGATATGGGCGAATATGGTCGCATGAGCAAGgttcttggat ... ttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtcttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
                                          ttcttac  putative branch site (score: 70)
                                          ttcttact  CT-rich tract
               taagtttgtctatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttggatcacttatttagttatagtcttcgatgcagtaagtttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG