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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggccttggcctatgaagaagtgcatgtacattttgcagcattgttttcccatgacattgtcttgtatcgagaggacttacatagatgccttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 15
ttggccttggcctatgaagaagtgcatgtacattttgcagcattgttttcccatgaca------ttgtcttgtatcgagaggacttacatagatgccttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG
     |     || |||||    ||  | |  || ||     | ||| |  | |  ||      || ||   ||| | | | |||||  |||||| || ||  ||||| |||||||| |||||||| ||||| || |||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||
----acccaatct-tgaagtctggctcgcaagttgtgattactggttgtttcctagcagtttttttatcccttattg-gtgtacttatttagatgtctacatgcagATCAATGAAGGTGATGGTGCCTTCTATGGTCCAAAAATTGATATTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAG

upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 15
ttggccttggcctatgaagaagtgcatgtacattttgcagcattgttttcc-catgacattgtcttgtatcgagaggacttacatagatgccttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG
               | |    ||||  || |||   | | |  ||| |     |||  || |||||  ||        |||  |   |      | |||||| ||||||||||| ||||| || || || ||||| ||||| ||| |||| | ||||||  | || |||||||| |||||||||||  |||||
---------------gtaactttgca-ataaattaccctgtaccgttctatatttgaagttctcttgcctctta-----ttatttgagtcatgctatacagATAAATGAAGGGGACGGTGCATTTTATGGACCAAAGATTGACATTAGTGTTTCTGATGCATTAAATAGGAAATTCCAGTGTGCAACATTACAG
















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|211046688|gb|FL336954.1|FL336954
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|32832908|gb|CD972586.1|CD972586
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATAAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|67033102|gb|CO461851.1|CO461851
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCANAAAT-GATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|113703092|gb|EE680596.1|EE680596
EST:     CTGAGCAACAATTGCCAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|211228557|gb|FL433549.1|FL433549
EST:     AACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: AACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|78092216|gb|DV520590.1|DV520590
EST:     TTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: TTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|22545540|gb|BU097899.1|BU097899
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATAAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|60339654|gb|DN206627.1|DN206627
EST:     ACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: ACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|32934180|gb|CF038992.1|CF038992
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATAAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|211228558|gb|FL433550.1|FL433550
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|32832310|gb|CD971988.1|CD971988
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATAAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|32834031|gb|CD973709.1|CD973709
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATAAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|50324858|gb|CO519984.1|CO519984
EST:     CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
EST: gi|32835314|gb|CD974992.1|CD974992
EST:     CTGAACAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG                         ATAAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG
genomic: CTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 284

AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 242

AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAGgtaccttcac ... cttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcccatgacattgtcttgtatcgagaggacttacatagatgccttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG
                              gacttac  putative branch site (score: 125)
                                          tgccttc  putative PPT
                                 ttacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggccttggcctatgaagaagtgcatgtacattttgcagcattgttttcccatgacattgtcttgtatcgagaggacttacatagatgccttcacacagATTAATGAAGGGGATGGTGCTTTCTACGGCCCAAAAATTGATATTGGTGTGTTTGATGCCCTTAAGAGGAAATTTCAGTGTGCAACCCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - ttgcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtat