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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgcttattccttctgtacagaacactcatttgtggttcttaagcatgctcgtgatgtatacagtacagaaccgtagcaaagctccttattgtgtcccggaattcttttttctttgttgaagtactcaacttaatcctctcttattacgtacctgcag

Basic information

species Zea mays
transcript GRMZM2G077278_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 2
GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgcttattccttctgtacagaacactcatttgtggttcttaagcatgctcgtgatg-tatacagtacagaaccgtagcaaagctccttattgtgtcccggaattcttttttctttgttgaagtactcaacttaatcctctcttattacgtacctgcag
|| ||||||||||||||||| ||||||||||||||||| |||||||| |||||||| |||||||||   |||||||  |||||||| |||||||||||||||   | || || |||| ||  |       |||    || || |  |  ||   ||  ||| || | | |   | |   ||   ||| ||| |    |||  |                                                            
GGCAAAGTGAAGATCGCGGAGCATATATTGACTGGTCACAAGGTGGCAATCAAGATCCTCAATCGCCGTAAGATCAAGAGCATGGAGATGGAAGAGAAAGgttggtactgatccctt-tgacccttttgttcaag-atgtttgtagaatatatacgaaatgatagatacttgggtaa-atatttaagatccatcacatgtttc------------------------------------------------------------

upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 2
GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgcttattccttctgtacagaacactcatttgtggttcttaagcatgctcgtgatgtatacagtacagaaccgtagcaaagctccttattgtgtcccggaattcttttttctttgttgaagtactcaacttaatcctctcttattacgtacctgcag
|| || || || || || |||||| |||||||||| |||||||| |||||||||||||| || ||    ||||| |  | |||||| |||||||| ||||||   |  || ||  || | || | ||   ||| ||||  |   |||   || || |  | ||          ||   |||      |    | | | ||| | | ||  ||||  |||                                           
GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttata-ttgtt--ttttataaataaatttcaattgtcat--ctaattgtggtcctttttta----------aattttag----attttccaatatttcctgcagtttgttttgtttt-------------------------------------------

upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ16445 (Selaginella moellendorffii), 5'ss of exon 1
GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgcttattccttctgtacagaacactcatttgtggttcttaagcatgctcgtgatgtatacagtacagaaccgtagcaaagctccttattgtgtcccggaattcttttttctttgttgaagtactcaacttaatcctctcttattacgtacctgcag
|| || |||||||||| ||| ||| |  | || || || ||||| || ||||||||||| ||||| | |||||| |||  |||||| |||||||||||||||    |   |    |  | |        |||||||   ||  ||         |                                                                                                           
GGCAAGGTGAAGATCGGGGAGCATGTCCTCACAGGCCACAAGGTTGCTATCAAGATTCTTAATCGGAGGAAGATTAGAGCCATGGACATGGAAGAGAAAGgtatgagaaaaaatatctttttt------ctcatttcctgtgtttcgatcgatgcag---------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 1
GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgcttattccttctgtacagaacactcatttgtggttcttaagcatgctcgtgatgtatacagtacagaaccgtagcaaagctccttattgtgtcccggaattcttttttctttgttgaagtactcaacttaatcctctcttattacgtacctgcag
|| || |||||||||| ||| ||| || | || || || ||||| || ||||||||||| ||||| | |||||| |||  |||||| |||||||||||||||              |  | | | || | |  |||     ||| |    | |  ||| |  |  |  | |||                                                                                         
GGCAAGGTGAAGATCGGGGAGCATGTACTCACAGGCCACAAGGTTGCTATCAAGATTCTTAATCGGAGGAAGATTAGAGCCATGGACATGGAAGAGAAAGgta-------------tgagaaaaaaatagtttttt-----tctcat---ttcctgtgtttcaatcgatgcag-----------------------------------------------------------------------------------------

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|91878198|gb|EB408155.1|EB408155
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|149109232|gb|EE190089.2|EE190089
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|71327271|gb|DR800259.1|DR800259
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|74240534|gb|DT648448.1|DT648448
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|149013919|gb|EE043417.2|EE043417
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|211110233|gb|FL282966.1|FL282966
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|211085855|gb|FL313546.1|FL313546
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|148954916|gb|EC900404.2|EC900404
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|78108756|gb|DV527173.1|DV527173
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|9255242|gb|BE345710.1|BE345710
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|9255371|gb|BE345839.1|BE345839
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|76012620|gb|DT939790.1|DT939790
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|31352455|gb|CD436812.1|CD436812
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAGGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
EST: gi|211104121|gb|FL354108.1|FL354108
EST:     CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAG                         TTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC
genomic: CAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATAC

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: 216

GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATACGCCTTTATGAGGTGATAGATACACCTGCTGATATCTGTGTTGTTATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATACGCCTTTATGAGGTGATAGATACACCTGCTGATATCTGTGTTGTTATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATACGCCTTTATGAGGTGATAGATACACCTGCTGATATCTGTGTTGTTATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgctt ... gtacctgcagTTAAGAGAGAAATCAAGATACTGAGATTATTTATGCATCCTCATATCATACGCCTTTATGAGGTGATAGATACACCTGCTGATATCTGTGTTGTTATGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgcttattccttctgtacagaacactcatttgtggttcttaagcatgctcgtgatgtatacagtacagaaccgtagcaaagctccttattgtgtcccggaattcttttttctttgttgaagtactcaacttaatcctctcttattacgtacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA