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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG

Basic information

species Zea mays
transcript GRMZM5G878139_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g41900.1 (Oryza sativa), 3'ss of exon 3
gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataat-ttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
|| ||||  |     || |||   |  ||| | |   | ||  |       | | |       |   |||   |||||| |||||||||| ||| ||   ||| || ||||||||||| ||||||||||||||||| || ||||| |||||||||||||| ||||| ||||| |||
gtgaggaatcagt--tttatagcacagttgatagtgcttacaat-------gttcaccatgtcatttattttgttacaaacttatctgaagaatctttgtagGGAATGAGCATGCACTTGTCATATCAAATCATCGGAGCGATATCGATTGGCTTATTGGGTGGATTTTGGCACAG

upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G12560.2 (Glycine max), 3'ss of exon 3
gtaaggagccctccattaatatttccattgt-ttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
    | |   |||   || ||||    | ||  |    |||||  |   |   |  |            ||| |||   |   | |||  |  ||||  |||||||||||||||| || || || || |||||  ||||||| |||||||||||| |||||||| | || || |||
----gtaagtctcttgtactattcatttagtgctaggctcaccccccatccccccaattctcgctcttcttgaattctgattctgtctaga--attttccagGTAAAGAGCATGCTCTTGTTATCTCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG

upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 3
gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
|||||   | ||      ||   |  | || | |   |||||  | | |   |  |            ||| |||   |   | |||  |  ||||  |||||||||||||||| || |||||||| |||||  ||||||| |||||||||||| |||||||| | || || |||
gtaag--tctcttgtactatgcatttagtgctag-gctcacccccct-ccccccaattttcgttcgtcttgaattctgattctgtctaga--attttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG

upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 3
------------------------------gtaaggag------ccctccattaatatttccat------tgtttgcattc--accttcatgcaagcttaaggaaaaaaagattggattacaa---gcttatctg-aataatttca----------------cagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
                               |||| |       |||||||||  | | |||||      ||| |||||||  | ||||  | |||   ||||   |     ||||   |  |   ||||   |  |||||||| |                ||||||||||||||||||| || |||   |||||  |||||||||||||||||||| |||||||| | |  || |||
gtaagccttttgttagcctatgatttagcactaagcaatttactccctccattc-tttctccatgtgttgtgtatgcattcttatcttctagaaaggaaaagggggaggttcttgggacaacatttgcttccatataataatttgattctgttttgtattatcagGTAAAGAGCATGCACTTGTGATAAGCAATCACAGAAGTGATATTGATTGGCTTGTTGGATGGGTTTCAGCTCAG

upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G32420.1 (Glycine max), 3'ss of exon 3
------------------------------------gtaaggagccctccattaatatttccattgtt--tgcattc--accttcatgcaagcttaaggaaaaaaagatt--ggattacaa--gcttatctg-aataatttca----------------cagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
                                            |||||||||  |   |   ||||   || ||||  | ||||  | |||   ||||    |     |  |||  |||   |||||  |  ||||||||                  ||||||||||||||||||| || |||   |||||  |||||||||||||||||||| |||||||| | |  || |||
gtaagtcttttgttagcctatgatttagcactaagcactttactccctccattctttcgtgtgttgtacatgtattcttatcttctagaaaggaaaaggggggaggttcttgggacaacatttgcttacatataataatttggttctgttttgtattatcagGTAAAGAGCATGCACTTGTGATAAGCAATCACAGAAGTGATATTGATTGGCTTGTTGGATGGGTTTCAGCTCAG

upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagg--agccctccattaatatttccattgtttgcattcaccttca---tgcaag---cttaaggaaaaaaagattgg--attacaa-gcttatctgaataatttcac--agGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
|||||   |       |||   | |   ||   || |      |||||   |  ||    | || | || ||   ||  |  | | ||  |  | ||  | || |||     ||| ||||| ||||| || ||| | |  ||||| ||||||||||||||||||||| | ||||||||  |||| |||
gtaagttcatatgcttattggcaatcaaatcagtttctgatgtcttcaagatataaaattcctatgtaagaacgaatctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG

upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G51260.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
               | || ||   || | | ||||   ||||       ||  |  | | | || ||||   ||  |   | || | ||  ||||||  || ||||| || ||||| ||| ||   |||||||||||||| ||||||||||||||||||||| |  |||| |||
--------------gtaaagat---caatttatgca---acctagtcttcagtatttgaatataatgattctttttaatcttgatattaa--atttca--gGGAAAGAACACGCACTTGTCTTAAGCAATCATCGAAGTGACATTGATTGGCTTATTGGATGGGTCATGGCTCAG

upper sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataa-tttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
                | | | ||       |    ||||| |     |     |  |   | |  |   |  |   || | |||   |||   ||| || |   | | |||  |||||||||| ||||||||  | |||||||| ||  ||||||| |||||||||||| |||||||| | ||||| |||
gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaatacattt--ttattggctaatgttggtgagtttttcagGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG

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|211257589|gb|FK979860.1|FK979860
EST:     TGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGG                         GTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGC
genomic: TGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGGgtaaggagcc ... aatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGC
EST: gi|211260012|gb|FK979863.1|FK979863
EST:     TGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGG                         GTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGC
genomic: TGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGGgtaaggagcc ... aatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGC
EST: gi|211257591|gb|FK979862.1|FK979862
EST:     TGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGG                         GTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGC
genomic: TGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGGgtaaggagcc ... aatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 167

GAAGCAAGCATTGATTTTTTCCTTCCTGATCCCAGAATAACTTCAGCTTATGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGGgtaaggagcc ... aatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 182

GAAGCAAGCATTGATTTTTTCCTTCCTGATCCCAGAATAACTTCAGCTTATGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGGgtaaggagcc ... aatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 157

GAAGCAAGCATTGATTTTTTCCTTCCTGATCCCAGAATAACTTCAGCTTATGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGGgtaaggagcc ... aatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 268

GAAGCAAGCATTGATTTTTTCCTTCCTGATCCCAGAATAACTTCAGCTTATGCTCTGCAGGTACAACTACATGCGGATGAGGAAACTTACCGATCAATGGgtaaggagcc ... aatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagcttaaggaaaaaaagattggattacaagcttatctgaataatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
                                   ttatctgaataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggagccctccattaatatttccattgtttgcattcaccttcatgcaagcttaaggaaaaaaagattggattacaagcttatctgaataatttcacagGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA