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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttcttgtcactacctccccctccaaagcattacagggatagtctattagtctttgcacacatttgatgatttttatcctattcttgtaaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 7
gtatcttcttgtcactacctccccctccaaagcattacagggatagtctattagtctttgcacacatttgatgatttttatcctattcttgtaaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG
         |||   | || ||   | ||| |  | |||    | | |    ||||| || |  |||||| ||| | ||||  |  | || |   || |||||||| |||||||| ||||||||||||||||||||||||||| |||||||||||| ||| || ||||  |||||||||||||| ||||| |||||||| |
------gtctgtggttcccaccattttcaa-gtttaacacttctggac----agtctctgaaggcatttgctgaatattatatttattttatt--ttccagATAGAAAGCAACATTGTTAGATGTCCTGATCCAGAATATGCACAGAAGATGATTGATGCAATCGATAAAGTACGAGTTAGAGGTGATTCGATTGGTGGTG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 7
gtatcttcttgtcactacctccccctccaaagcattacagggatagtctatt---agtctttgcacacatttgatgatttttatcctattcttgtaaatt--tcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG
      | |||  | ||| | |   |        |  ||    || | |  |   | |  |    |  | ||  || |||      | || ||| || ||   ||||| ||||| ||||| ||| ||||||| || || ||||||||||||||||||||  |||| |||||| | || ||||| ||||| |||||  ||||||| |
------tattgagaatactttctattgatgtttttatcattattatttttcttgcaattctgaagccaaattcctggtttaccatttttttttggaatttgtccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAATATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 7
gtatcttcttgtcactacctccccctccaaagcattacagggatagtctat-tagtctttgcacacatttgatgatttttatcctattcttgtaaattt---cagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG
     ||       | |  |  |      |   ||||  |  |||   ||| | |    | |   |  |||||| || ||| | | || ||   |||||   ||||| ||||| ||||| ||| ||||||| || || || |||||||||||||||||  |||| |||||| | || ||||| ||||| |||||  ||||||| |
----atttacaatgcaatgtttcaaattgactaattattgttataacttatattgataatactttctattgatg-ttcttaccattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 7
gtatcttcttgtcactacctccccctccaaagcattacagggatagtctattagtct-ttgcacacatttgatgatttttatcctattcttgtaaatt-tcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG
     || || |   |   |  |  |   |  | ||   |  ||| |||  |  |   ||| | |  |   || | | || ||    | | | | |||  ||||||||||| || || || || || || ||||| |||||||||||||||||||||||||| |||||| | || || || || ||||||||  |||| || |
---cttttttctttttctttttcttttttagtcctttttgttatattcttatgatgaattgtagaattcccattaatgttctctctctatggaacattgccagATAGAGAGTAATATTGTGAGGTGCCCAGATCCTGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTG

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|149088514|gb|EE177624.2|EE177624
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|211540751|gb|FL105309.1|FL105309
EST:     ATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: ATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|149070137|gb|EE158538.2|EE158538
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|213172541|gb|FM189510.1|FM189510
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|32808278|gb|CD960512.1|CD960512
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|149015775|gb|EE045474.2|EE045474
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|71442663|gb|DR823713.1|DR823713
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATC
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATC
EST: gi|148963945|gb|EE015067.2|EE015067
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCTTGATCCAGACTATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|78089034|gb|DV517427.1|DV517427
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
EST: gi|67042195|gb|CO468450.1|CO468450
EST:     TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG
genomic: TCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATG

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: 46 (upstream exon), 49 (downstream exon)
Score: 262

ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 590

ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 511

ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 599

ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACATgtatcttctt ... taaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattagtctttgcacacatttgatgatttttatcctattcttgtaaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG
                   atttgat  putative branch site (score: 599)
                                       ttcttgt  putative PPT
                   atttgatgatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttcttgtcactacctccccctccaaagcattacagggatagtctattagtctttgcacacatttgatgatttttatcctattcttgtaaatttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG