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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactatttgcagcttaagatcctacctacctggtgcag

Basic information

species Zea mays
transcript GRMZM2G119169_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0010g03380.t01 (Vitis vinifera), 5'ss of exon 4
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgc---tatgctatgaacaggttactatttgcagcttaagatcctacctacctggtgcag
|||||||| ||||| ||| | |||||  | || ||||| |||||||||||||| ||||| ||  ||||| | || ||||| ||||||||  | |||||||||||||  || |    |  ||  | ||   | ||  |||      || |||  ||         | | |   |   |   ||||
AAAGGTCTGGATGTTGATTCACTCTACATATCTCACATCCAAGTGAACCAGGCACAGAAACAAAGGCGCCGCACATACCGGGCTCATGGAAGAATCAACCgtaagtttgtttcctttcaaatctagcatttgtgtaatggttgttttcctaaatgttaacaggaaccttctatttgtttggcag

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 4
lower sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 3
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgcta-tgctatgaacaggt-tactatttgc----agcttaag---------------atcctacctacctggtgcag
|||||||||||||| || || ||   ||| || ||||||||||| |||||||| ||||| |||||  |  | |||||||| |||||||| || ||||||||||||| |  |    |||  | || | ||    ||||| |   | | ||||| |     |||  |||               ||| ||||||  |  ||   
AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatcccatcgttttacttggttagctttatgatcttctgtcctattagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga--

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 4
lower sequence: PP1S97_78V6.3 (Physcomitrella patens), 5'ss of exon 3
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactat-ttgcagcttaagatcctacctacctggtgcag--------------------
|| ||||| ||||| || || ||   ||| |||||||||||||| |||||||| |||||||||||  |  | || ||||| || || ||||| |||||||||||||  |  |   || | | ||   | |  | |   | |  |  | | || | | |  |  | | | |      | |                       
AAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggcgt--tgtcggacttttgttttttttcctctgacttttctgtttcggttatattttcgatcagttctgggtgacggcaggagtgccgagtctc

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 4
lower sequence: EFJ21308 (Selaginella moellendorffii), 5'ss of exon 4
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactatttgcagcttaagatcctacctacctggtgcag
|||||  | || |  |||||||| ||||| || ||||| ||||| |||||||| ||||||||||| || ||||| ||||| |||||||| || ||||| |||||||     |||||||     ||| |   |||  | | |  | |     |  ||||         |             
AAAGGCTTGGACGCGGATACCCTGTATGTCTCGCACATCCAAGTCAACCAGGCACAGAAGCAGCGCCGGAGGACTTACCGAGCTCATGGCCGGATCAATCgtaagtgg---tgaagttcttcctcgttgatctagaagctgactgcg----gtggctttgtgcttggcag-----------

upper sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 4
lower sequence: EFJ26852 (Selaginella moellendorffii), 5'ss of exon 4
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactatttgcagcttaagatcctacctacctggtgcag
|||||  | || |  |||||||| ||||| || ||||| ||||| |||||||| ||||||||||| || ||||| ||||| |||||||| || ||||| |||||||     |||| |  |       |  |||  ||       |   |||   ||||   |                   
AAAGGCTTGGACGCGGATACCCTGTATGTCTCGCACATCCAAGTCAACCAGGCACAGAAGCAGCGCCGGAGGACTTACCGAGCTCATGGCCGGATCAATCgtaagtgg---tgaattctattcctctttggcttagaggcttacatcgttttgtgcttggcag------------------

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|37390893|gb|CF632684.1|CF632684
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|5847620|gb|AW000699.1|AW000699
EST:     GGCTCAAAAGCAGCGGCGCAGGACCTACCGGGCTCATGGGCGCATCAACC                         CTTACATGTCCTTCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|67011457|gb|CO440206.1|CO440206
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|4885932|gb|AI677052.1|AI677052
EST:     AGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: AGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|9952004|gb|BE638587.1|BE638587
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|60345876|gb|DN212849.1|DN212849
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|32848019|gb|CD987700.1|CD987700
EST:     TGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: TGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|30704734|gb|CD058588.1|CD058588
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|33097211|gb|CF057171.1|CF057171
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTNNNNNNNGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|50335900|gb|CO531026.1|CO531026
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|101386822|gb|EB815428.1|EB815428
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|211381023|gb|FL000683.1|FL000683
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|5525695|gb|AI861588.1|AI861588
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCCCATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|60349795|gb|DN216768.1|DN216768
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|32837215|gb|CD976893.1|CD976893
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|213173920|gb|FM195799.1|FM195799
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|60356912|gb|DN223885.1|DN223885
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|14701011|gb|BI233429.1|BI233429
EST:     AGCGGCGCAGGACCTACCGCGTTCATGGACGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATC-AAGCTCATCTTGTCAGAGAAGGAA
genomic: AGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAA-CTCATCTTGTCAGAGAAGGAA
EST: gi|32945522|gb|CF050341.1|CF050341
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|32934714|gb|CF039526.1|CF039526
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|29544312|gb|CB604692.1|CB604692
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|211140525|gb|FL058263.1|FL058263
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|67011073|gb|CO439822.1|CO439822
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
EST: gi|211372347|gb|FL430779.1|FL430779
EST:     GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACC                         CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAG

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), 41 (downstream exon)
Score: 373

AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 249

AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 169

AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 193

AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagt ... cctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactatttgcagcttaagatcctacctacctggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC