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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgtttttatctgtgtttttaatttttttttctgagtgccatctttttattttatcccttaatgactcacataattactgccacttattcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA

Basic information

species Zea mays
transcript GRMZM2G143725_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143725_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g04020.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------gtatcgtttttatctgtgtttttaatttttttttctga--gtgc--catctttttatt--ttatccctt--aat---gactcacataattactgccact-tattcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA
                                          | ||| | ||| ||| |||   | ||  | | | ||    ||||  ||| || ||||   |||| | ||  | |   || ||| | || | |      |  ||||||| || |||||||||||||||| ||||||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || || ||||| |||||||
gtatgtgctatttgttttgcagtttgatttcaatcacttaggggatcatatttttctctgtaactcataatatgtactagtggtgcagcatattcttataggttatgctttgtagtttggattcaaacaaattcaatgcttgcattctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATA
















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: 149

TGTTGCTCCAACAGAATATATGGTGCGGCCACCGATGCCGCCGTCCTATTTCTTTCTTATTGACGTGTCAGTGTCTGCAGTTCGAAGCGGATTGCTTGAGgtatcgtttt ... attcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 123

TGTTGCTCCAACAGAATATATGGTGCGGCCACCGATGCCGCCGTCCTATTTCTTTCTTATTGACGTGTCAGTGTCTGCAGTTCGAAGCGGATTGCTTGAGgtatcgtttt ... attcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

TGTTGCTCCAACAGAATATATGGTGCGGCCACCGATGCCGCCGTCCTATTTCTTTCTTATTGACGTGTCAGTGTCTGCAGTTCGAAGCGGATTGCTTGAGgtatcgtttt ... attcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

TGTTGCTCCAACAGAATATATGGTGCGGCCACCGATGCCGCCGTCCTATTTCTTTCTTATTGACGTGTCAGTGTCTGCAGTTCGAAGCGGATTGCTTGAGgtatcgtttt ... attcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttattttatcccttaatgactcacataattactgccacttattcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA
                      gactcac  putative branch site (score: 127)
                                       ccacttattctttt  putative PPT
                                           ttattctttta  TA-rich tract