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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattcttttatgcaccacccttattccccccccccccccccccctcccccccccacacacacacaccagtttctaacttctggctccccttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 3'ss of exon 8
gtaatattcttttatgcaccaccctt-attccccccccccccccccccctcccccccccacacacacacaccagtttctaacttctggctccccttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG
|||||||| | |   |    ||| ||   |  |  |         |     |    |             |  |  | |||||| ||  | | |||||| ||||||| ||||||||||||||||| || || ||  |||||||||| |||||||| || || || || |||||| |||| || |||||||||||| ||| ||| 
gtaatattatctacagagataccttttgctgactgcttggatgatcaaaagcagtacatctctttgttggctggcctgtaacttgtg-tttctcttttggacagGTAACTTTTCATATTTTTGAAGTTTATGGCCCCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGTACAAGCAGATGATTT

upper sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 8
gtaatattcttttatgcaccaccctt-attccccccccccccccccccctcccccccccacacacacacaccagtttctaacttctggctccccttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG
|||||||| | |   |    ||| ||   |  |  ||        |     |    |             |  |  | |||||| ||  | | |||||| ||||||||||||||||||||||||| || || ||  |||||||||| |||||||| || || || || |||||| |||| || ||||| |||||| ||| ||| 
gtaatattatctacagagataccttttgctgactgcctggatgatcaaaagcagtacatctctttgttggctggcctgtaacttgtg-tttctcttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT
















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|86470328|gb|DY236698.1|DY236698
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|18179571|gb|BM380781.1|BM380781
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|211295447|gb|FL439736.1|FL439736
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|78113030|gb|DV531424.1|DV531424
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|71313247|gb|DR793147.1|DR793147
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|148971663|gb|EE022386.2|EE022386
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGGGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|50331764|gb|CO526890.1|CO526890
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|60342765|gb|DN209738.1|DN209738
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|76013820|gb|DT940990.1|DT940990
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|60341702|gb|DN208675.1|DN208675
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATCGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|78091450|gb|DV519824.1|DV519824
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|211502356|gb|FL413772.1|FL413772
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|78022213|gb|DV490600.1|DV490600
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|211389689|gb|FL031640.1|FL031640
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|110482572|gb|EE011367.1|EE011367
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|60393918|gb|DN226788.1|DN226788
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|37374451|gb|CF623583.1|CF623583
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|4572984|gb|AI586633.1|AI586633
EST:     AGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|6056893|gb|AW091298.1|AW091298
EST:     GTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: GTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|101388963|gb|EB816463.1|EB816463
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|78077260|gb|DV505694.1|DV505694
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|76016276|gb|DT943446.1|DT943446
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
EST: gi|15100603|gb|BI396394.1|BI396394
EST:     AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGCCAA                         GTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA
genomic: AAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGA

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), 47 (downstream exon)
Score: 160

CTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 300

CTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 315

CTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 219

CTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAATGTCGGGGGGAGTGGAACCAGAAGTTGACAAgtaatattct ... ttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccccccccacacacacacaccagtttctaacttctggctccccttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG
                          ttctaac  putative branch site (score: 219)
                                cttctggctccccttt  CT-rich tract
                         tttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattcttttatgcaccacccttattccccccccccccccccccctcccccccccacacacacacaccagtttctaacttctggctccccttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT