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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatttgccaataactctatgctgtgtgtgttcaattgctagttcttctgctggaatttgatttttcttttgccttaatatttctaatgaaaaaaatcctttttttcccgaacatattacaatatgtttttctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA

Basic information

species Zea mays
transcript GRMZM2G160702_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 4
gtaagaatttgccaataactctatgctgtgtgtgttcaattgctagttcttctgctggaatttgatttttcttttgccttaatatttctaatgaaaaaaatcctttttttcccgaacatattacaatatgtttttctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA
                                || |       ||||            ||  |||  |   |||||||||   |   |  |  | | ||    |||||||         |||   || ||||  ||| |||||||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||||
--------------------------------tgattttcctttagtgaactcaacatgat--gatgatgaatttgccttacagtaaattttccatagaacttgttttttc---------ttatggtaagtttgcctt-ggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGATTTCAAGTGTCATGAAGGCCAGATTCAGTGCATAGATTTCCATCCCCATGAGTTCCTTCTGGCAA

upper sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaatttgccaataactctatgctgtgtgtgttcaattgctagttcttctgctggaatttgatttttcttttgccttaatatttctaatgaaaaaaatcctttttttcccgaacatattac-aatatgtt--tttctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA
                                        ||  |  | | | |||      | |  | | | | |  ||||  ||   | ||       |  || ||||    | ||| || | ||||   |   | |||   ||||| ||||||||||| ||||||||||| || || || |||||  |||||||||| ||| | |||||||||||||| || || || || || || |||||||
----------------------------------------tgaaaaatatgcagcttcccacttacatgtttgtgg--ttaaccttgtaagtg-----tttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
















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: 247

CATCCATACATACAAAGGTCACACACGAGGGGTGAACACTATTAGATTTACACCCGATGGGCGGTGGGTTGTGTCTGGTGGCGAAGATAATATAGTAAAGgtaagaattt ... tctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 60

CATCCATACATACAAAGGTCACACACGAGGGGTGAACACTATTAGATTTACACCCGATGGGCGGTGGGTTGTGTCTGGTGGCGAAGATAATATAGTAAAGgtaagaattt ... tctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CATCCATACATACAAAGGTCACACACGAGGGGTGAACACTATTAGATTTACACCCGATGGGCGGTGGGTTGTGTCTGGTGGCGAAGATAATATAGTAAAGgtaagaattt ... tctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 260

CATCCATACATACAAAGGTCACACACGAGGGGTGAACACTATTAGATTTACACCCGATGGGCGGTGGGTTGTGTCTGGTGGCGAAGATAATATAGTAAAGgtaagaattt ... tctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaaaaaaatcctttttttcccgaacatattacaatatgtttttctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA
 ttctaat  putative branch site (score: 260)
                                       tgtttttcttt  putative PPT
                            atattacaatatgttt  TA-rich tract