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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttcctgatgtcttgaattcttctttaattcagcagacttgtgtactcatatatgtaccatgccgttctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 9
gtaagtcttcctgatgtcttg-aattcttctttaattcagcagacttgtgtactc------atatatgtaccatgc---cgttctttgttttga-tcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT
|||||| |||||||  | ||| || || |||   ||  |     ||  |  ||||      |||||  | |  | |   |   |||| | ||||  |||| |  |     || | ||||||||||||||||||||||||| ||| |||||||| || ||||||||||| ||||| ||||||||||| ||
gtaagtgttcctgagttattgcaaatcctctaacatgtaatctgctgtttcactcttatgcatatagatgctttacttacagcctttatgttgaaccatttctattcatgttcatagGTCACTTCAAGGAAATAGACTGACTGGGAAAATTCCAGATGTGATTGGCCTGATGCAAGCTCTTGCTGTTCT

upper sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G38730.1 (Glycine max), 3'ss of exon 10
------------------------------------------------------------------gtaagtcttc-ctgatgtcttga---attcttctttaattcagcagacttgt--gtactcatatatgtaccatgccgt-tctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT
                                                                   |  |||||| ||    ||||||   |   || |||  ||    |   |  |  ||  |  |||||| |  | |     | | ||||    |       || ||  |    ||||||||||||||||||||||| | ||| || ||||| |||||||||||  | ||||| || |||||  |  |
gtgagtactttgactgtgaagttattgttttaatgttacacttagcactactatgaatcacttgctttctgtcttctctctcttcttgacaaaggtttattttgtttgagaatgtgattggtcatgttatatggagaaggataagtatatgttcacgtatgaatgttttttctgcctagGTCACTTCAAGGAAATAGACTAACTGGGAAGATTCCAGAAGTGATTGGTTTAATGCAAGCCCTTGCAATATT

upper sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT5G07180.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtcttcctgatgtcttgaattcttctttaattcagc--agacttgtgtactcatatatgtaccatgccgttctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT
                     || | || || |   || |  | |||| |||     |   |  | |||| |  | |     || |    ||    ||| | || |||||||||||||||||| |   ||| ||||| |||||| ||||||||||| || |||||||||||||||||  |
-------------------gtaagtattgttaagaccatcttacacttttgtgtggtttgttaaagcatgtcaatatgg---ttaagtggtgatgggttctcttgcagGTCACTTCAAGGAAACAAGTTGACTGGCAGAATTCCGGAAGTGATTGGTCTGATGCAGGCTCTTGCTGTATT

upper sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtcttcctgatgtcttgaattcttctttaattcagcagacttgtgtactcatatatgtaccatgccgttctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT
           ||| || ||||   ||  ||||  | ||     ||   |    | ||   || ||||| ||| || |  |||   |||  |||  | ||||  ||||||||||||||||| ||| |||  || | |||||| ||||| ||||| || |||||||||||||||||  |
----------gtga-gtattgagc-ctcttttaccttag-----tttcatcagtaaattgttaacatgcggttatt-gaattgtgtatt--attact-ttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT

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|148934014|gb|EC878019.2|EC878019
EST:     ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT                         GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTG
genomic: ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTG
EST: gi|148940443|gb|EC885241.2|EC885241
EST:     ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT                         GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
genomic: ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
EST: gi|149079906|gb|EE168912.2|EE168912
EST:     ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT                         GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
genomic: ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
EST: gi|148964982|gb|EC906062.2|EC906062
EST:     ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT                         GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
genomic: ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT                         GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
genomic: ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCT
EST: gi|148957491|gb|EC903572.2|EC903572
EST:     ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT                         GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGA
genomic: ATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 546

GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 48

GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 345

GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACTgtaagtcttc ... tgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatatatgtaccatgccgttctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT
                           ttttgat  putative branch site (score: 345)
                                            ttgtttt  putative PPT
                       tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttcctgatgtcttgaattcttctttaattcagcagacttgtgtactcatatatgtaccatgccgttctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG