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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactcatctatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC

Basic information

species Zea mays
transcript GRMZM2G079196_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
gtatactcatctatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
   || |||  |   || |||||||||    |    | |||      |   | ||| || | ||      |  |  |  ||| || | | |  ||||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| |||||||| |||||
--gtaatcaaatcatctgcatttcttttc-cattttaatttcg---tatattgataaatttagaacttcctcatccttttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 7
-gtatactcatc-tatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
   | | | | | | ||  |    | |||    ||| |   || |    ||  |  | | | |  ||  | |  | |    |  ||| |     || | || || ||||| || ||||| ||||||||||| |||||||| |||||||||||||| || ||||| |||||
ctgagatttagcatttagcttgactatttggaaacaaaccattcaagcaaccttttttcttttgtattta-acttgtaacatagtttctatttcgtgtcagGTACCTTGTTCTGGCCAACATGTTGATGGAGTCTGAAGTAAATCCTTTTGATGGGCAGGAGGCTAAGCC

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 7
gtatactca--tctatacttcatttctttctgtacagaagttttagaacactctaata-catatcgataaatatatttttggttt--tttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
 | | || |  | ||   || |    |  || |    || |   | | || || |  | | | |   | | || | || |    |  ||  |      | | || || ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| || ||||| |||||
-tttcctgagatttagcatttaagcttgactatttgaaaat---aaaccattcaagcaaccttttttttattaaacttgtaacatagttgctattacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 7
gtatactcatctatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgcc-gtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
  || |  |||  |     ||       |  | | ||    | ||| ||   | |   |     | |     | |    |  || ||     ||  | || || ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| || || || |||||
aaatccaaatcccttacatatcatgacttcaaaataaaccattgaatacatcattctttgcttttgacatcttgtacaataattgttatttatgagtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGGCAGGAAGCTAAGCC

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 7
gtat-actcatctatact-tcatttctttctgtacagaagttt--tagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
|||  | |  | |    | ||| |    | | || | | |  |  |  | || |    | | | | || |  |       |  || || ||    ||  | ||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||| || || |||||
gtaggaattgtttgggttctcagtaggatttataaacatgcatggttaagcatttgtttgc-ttttgacatcttgtacaataattgttatt--tatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 7
-------gtatactcatctatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
        |    | |    |      |  ||||||||   ||    |   ||||   ||     ||  |||   | | |||||  || |||| ||  || |  || |||||||| || || |||||| ||||||| || ||||||||||| |||||||| |||||||| |||||
gagcattattcgattactcttgtccagtaactttctgt---gatcggtccaaacatgttagagt-taatgatctttgt-tttttttttcttttggctatgcaa-agGTATCTTGTTCTGGCGAATATGCTGATGGAGTCAGAAGTGAATCCGTTTGATGGCCAAGAGGCAAAGCC

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|211507840|gb|FL110003.1|FL110003
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGCAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|67023333|gb|CO452082.1|CO452082
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAATTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|211507839|gb|FL110002.1|FL110002
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|211507837|gb|FL110000.1|FL110000
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGCAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|32938723|gb|CF043542.1|CF043542
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|32845980|gb|CD985661.1|CD985661
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|18659527|gb|BM500385.1|BM500385
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|211507835|gb|FL109998.1|FL109998
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGCAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
EST: gi|211507838|gb|FL110001.1|FL110001
EST:     TTCAAGAACTACGATGAAGCAGGCAATCCACGCAGAATCCAATGCCTAAA                         ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA
genomic: TTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGA

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: 169

ATATGGCTGAGAGGCAGTGGGCTGAGGCTGCGACTGATTTCTTTGAAGCTTTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

ATATGGCTGAGAGGCAGTGGGCTGAGGCTGCGACTGATTTCTTTGAAGCTTTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

ATATGGCTGAGAGGCAGTGGGCTGAGGCTGCGACTGATTTCTTTGAAGCTTTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156

ATATGGCTGAGAGGCAGTGGGCTGAGGCTGCGACTGATTTCTTTGAAGCTTTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcat ... cgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
    ctctaat  putative branch site (score: 156)
                                   ttttttttgcc  putative PPT
       taatacatatcgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactcatctatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG