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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcagtgatttatttcccaagtcaatgctcagtcatgaaagcgtctctgtgacttttttgtttgttatgataaattatgataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG

Basic information

species Zea mays
transcript GRMZM2G005036_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g44916.1 (Oryza sativa), 3'ss of exon 4
gtaagattcagtgatttatttcccaagtcaatgctcagtcatgaaagcgtctctgtgacttttttgtttgttatgataaattatgataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG
|||||| | ||| ||||||    || || |||  |||||||   | || ||| | | ||  |||      || |      |  ||| ||||||||||| | |||||||| ||||||||||| ||||||||||||||| |||| || |||| | || ||||||| | |||||||||||| || ||||||||  | |
gtaagactaagttatttat----catgttaatagtcagtcacagatgcctctgtttcaccctttgac--attcttgcttgtgctgagaaatgtagGAAAACTACACTGCCCCCAGGATGGTACTTGCAGCATCAGGAATTGAGCACGATGAGTTGGTTTCAGTCGCAGAACCACTTCTATCAGACCTTCCCAGTG

upper sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------gtaagattc--agtgatttatttcccaagtcaatgctcagtcatgaaagcgtctctgtgacttttttgtttgt-tatgataaatt---------atgataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG
                                                      ||  |||  |||  || |||||     ||  || |   ||||       |   | |    ||||||  ||| |    | ||||          |  | | |  ||||  ||||||||||||| |||||||| ||||| || || |||||||| ||||| | | |  | ||  ||| ||| |||||| | ||| | |||||  | |
gtaagacaaagaaaaacttataaatactgcatacagaattaattttttttgctcaatcttctcagtctttcatttcatgtttctttgtttt-tcattttccttttggtttcctctttttgcgtgtgttctctgaattcctttttctgtctttatttcagGAGAATTACACTGCTCCTAGGATGGTCCTTGCGGCTTCTGGAGTTGAACATGAAGAGTTTTTGTCCATTGCAGAGCCACTTGTTTCTTATCTTCCCAGTG
















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|71764445|gb|DR962382.1|DR962382
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|31356317|gb|CD440674.1|CD440674
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|89761459|gb|DY689465.1|DY689465
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|31358559|gb|CD442916.1|CD442916
EST:     AATCTGCTGTAAACCGGGTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|31354401|gb|CD438758.1|CD438758
EST:     ATCTGCTGATAA-CCGGTTGGATGTTAGCAGCTGGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAG
genomic: ATCTGCTG-TAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAG
EST: gi|31353102|gb|CD437459.1|CD437459
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|76912595|gb|DV164810.1|DV164810
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCC
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCC
EST: gi|31354663|gb|CD439020.1|CD439020
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|148965824|gb|EE016713.2|EE016713
EST:     ATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGATTTTTGT-GCT                         GAACATTACACTGCTC
genomic: ATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTT-GTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTC
EST: gi|148944905|gb|EC890064.2|EC890064
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACT
EST: gi|71438038|gb|DR819088.1|DR819088
EST:     GGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: GGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|78106581|gb|DV524999.1|DV524999
EST:     AATCTGCTGTAAATCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAG
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAG
EST: gi|19822381|gb|BQ048405.1|BQ048405
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|31349354|gb|CD433711.1|CD433711
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|211159959|gb|FL410900.1|FL410900
EST:     AATCTGCTGTAAACCGGT-GGATGT-AGCAGCTTGGAGGATTTTGT-GCT                         GAACAT--CACTGCTCCCAG
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAG
EST: gi|30031572|gb|CB833423.1|CB833423
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|211246196|gb|FL443898.1|FL443898
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT

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: 597

TCATTCGGTTGGATATTCCGGGGCACTGGCAAAACCTTTGATGGCTTCAGAATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 616

TCATTCGGTTGGATATTCCGGGGCACTGGCAAAACCTTTGATGGCTTCAGAATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG


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

TCATTCGGTTGGATATTCCGGGGCACTGGCAAAACCTTTGATGGCTTCAGAATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 771

TCATTCGGTTGGATATTCCGGGGCACTGGCAAAACCTTTGATGGCTTCAGAATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaagcgtctctgtgacttttttgtttgttatgataaattatgataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG
                   ttttttgtttgttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattcagtgatttatttcccaagtcaatgctcagtcatgaaagcgtctctgtgacttttttgtttgttatgataaattatgataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCATGATGCGCTGATTTCAGTTGTAGAACCACTTCTGTCTGACCTTCCGTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT