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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataaaatatactgctgtgctggaaagtctaatagactccaatatgtaccttccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG

Basic information

species Zea mays
transcript GRMZM2G051050_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g38950.2 (Oryza sativa), 3'ss of exon 4
------------------gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataaa----atatactgctgtg--ctggaaagtctaatagactccaatatgtaccttc--------cctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
                   |  |  ||| | |  | | | |   |  ||     |       | ||||       || ||  | | |   ||||||| ||| | |     |  ||| | || |         ||| | |||| ||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||| |||||||||| | |||||| ||| |||
gtaggtcactgagtccaaatttccttttttttttaatataaaaagctagttttattggaggctaggatttttcttatttagcgtttttatctggaaaatctgacaagaagccgtatctgccatttctgggctccttacagGACTTGCCTAGAACTTTTCCAGGTCATCCTGCTTTAGACGAGGATGGAAGAAATGCTTTGAGACGTTTGCTTCTAGCTTATGCTAGACACAATCCAGCAG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 4
gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataa-aatatactgctgtgctggaaagtct----aatagactccaatatgtaccttccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
|||  || || || | ||||   |      |  | |  || | |     ||    |||    || |     |   |||    | ||| ||   ||   | | |        ||||| ||||  |||| |||||||||||||||||||| || |||||||| ||||||||||||||||| || ||||  || |||||   ||| ||||| ||||
gtatttgcttttg-atatttcatccttattgttcttaatactgtgatattattggtatgacactttaaacaagtttcttcttagtagtctattatcattgcttgtttgtgcagGATCTGCCTCGAACATTTCCTGGTCATCCTGCTTTGGACGAGGATGGTAGAAATGCTTTGAGACGATTACTTACTGCATATGCTCGACATAACCCCTCAG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 4
gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataaaatatactgctgtgctggaaagtct------aatagactccaatatgtaccttccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
|||  || || || | ||||   |      |  | |  || | |    || |    ||   || |      |||| |      | ||| |    ||   | | |     |  ||||| ||||  |||| |||||||||||||||||| | || |||||||| ||||||||||||||||| || ||||  || |||||   ||| ||||| ||||
gtatatgcttttg-atatttcacccttattgttcttaatactgtg-atattattggtatgactctttaaacaagtttcttcttagtagtccattatcattgcttgtttgcgcagGATCTGCCTCGAACATTTCCTGGTCATCCTGCTCTGGACGAGGATGGTAGAAATGCTTTGAGACGATTACTTACTGCATATGCTCGACATAACCCCTCAG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataaaatatactgctgtgctggaaagtctaatag-actccaatat-gtaccttccct----catagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
||||   |  |  |  |||    |   ||  | |  | | |  |   |||  |   |     | |||||  ||||  |  || | ||  ||   ||  |||   |     | |||| || ||  | || |||||||||||||||||| ||||||| ||||| ||||||||| |  | || |||||||  |||||||| |  || || || || |
gtagtactcaaaatttattca-gccttgaccctctctatgtagt---gatgcagcgtggc-ttatgctg--aagttgatcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtagctgtttatgtacattttcacggggaagcaccttgtattttttggat---aaaatat-actgctgtgctggaaa-----gtctaatagactccaatatgtaccttccctcat--agGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
                             |||     ||   |  ||||||| | |    |    |  | |      ||   ||   ||   | ||   ||  |||     |  | |  ||    || |   |  || |   ||  ||||||||||  |||| || || |||||||||||| ||||||||||||| |||||||||||||| || || ||||  || |||||   ||||||||| || |
gtcattacatgcatatgctttgaaatttagtactcaatttctttgattttcaggtgttgcctttgttaaatccaaaaatctcaagtcattgttactaatctctaaatgcaggatttactgatcaaaaaaaaaaaatttctaaatgcagGATTTGCCTCGAACATTCCCAGGTCATCCTGCTCTAGATGAGGATGGTAGAAATGCTTTGAGGCGTTTACTTACGGCATATGCTCGACACAACCCCTCTG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ22778 (Selaginella moellendorffii), 3'ss of exon 3
gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataaaatatactgctgtgctg-gaaagtctaat--agactccaatatgtaccttccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
                                                           | || | |   || ||| ||||  | | ||   |   |   |||     ||||| || ||  ||||||||||||||||||| ||| ||||||| |||||  | || || ||| |  |  |  | |  || || ||   ||| || ||    |
----------------------------------------------------------gtactataccatgatagtataatgtaaattcagttcgatgttttctggtgtagGACTTACCGCGAACTTTTCCTGGTCATCCAGCTCTAGATGAAGATGGTCGGAACGCATTGCGCAGGCTTTTGACTGCATACGCACGACATAATCCTGATG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ30863 (Selaginella moellendorffii), 3'ss of exon 3
gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataaaatatactgctgtgctg-gaaagtctaat--agactccaatatgtaccttccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
                                                           | || | |   || ||| ||||  | | ||   |   |   |||     ||||| || ||  ||||||||||||||||||| ||| ||||||| |||||  | || || ||| |  |  |  | |  || || ||   ||| || ||    |
----------------------------------------------------------gtactataccatgatagtataatgtaaattcagttcgatgttttctggtgtagGACTTACCGCGAACTTTTCCTGGTCATCCAGCTCTAGATGAAGATGGTCGGAACGCATTGCGCAGGCTTTTGACTGCATACGCACGACATAATCCTGACG

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|78115424|gb|DV533812.1|DV533812
EST:     CTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAG                         GATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGA
genomic: CTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAGgtagctgttt ... tccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGA
EST: gi|32834207|gb|CD973885.1|CD973885
EST:     CTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAG                         GATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGA
genomic: CTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAGgtagctgttt ... tccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGA

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), 48 (downstream exon)
Score: 96

TTATGATAATCTGGCAGCAGAGGGTGAATTAGATAACAAACGTTCAGATTCTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAGgtagctgttt ... tccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 24

TTATGATAATCTGGCAGCAGAGGGTGAATTAGATAACAAACGTTCAGATTCTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAGgtagctgttt ... tccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 37

TTATGATAATCTGGCAGCAGAGGGTGAATTAGATAACAAACGTTCAGATTCTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAGgtagctgttt ... tccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 46

TTATGATAATCTGGCAGCAGAGGGTGAATTAGATAACAAACGTTCAGATTCTCGAACCTCGGAAGGTGTTCACGAGAAGTGGATTGGACAAATAGAGAAGgtagctgttt ... tccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatactgctgtgctggaaagtctaatagactccaatatgtaccttccctcatagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG
                    gtctaat  putative branch site (score: 46)
                                        taccttccctc  putative PPT
                                  aatatgta  TA-rich tract